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wwPDB EM Map/Model Validation Report i
wwPDB EM Map/Model Validation Report O i Sep 20, 2016 04:49 PM EDT PDB ID : 3JBH EMDB ID: : EMD-1950 Title : TWO HEAVY MEROMYOSIN INTERACTING-HEADS MOTIFS FLEXIBLE DOCKED INTO TARANTULA THICK FILAMENT 3D-MAP ALLOWS IN DEPTH STUDY OF INTRA- AND INTERMOLECULAR INTERACTIONS Authors : Alamo, L.; Qi, D.; Wriggers, W.; Pinto, A.; Zhu, J.; Bilbao, A.; Gillilan, R.E.; Hu, S.; Padron, R. Deposited on : 2015-09-01 Resolution : 20.00 Å(reported) Based on PDB ID : 3DTP This is a wwPDB EM Map/Model Validation Report for a publicly released PDB/EMDB entry. For rigid body tted models, validation errors reported here could stem from errors in the original structure(s) used in the tting. We welcome your comments at [email protected] A user guide is available at http://wwpdb.org/validation/2016/EMValidationReportHelp MolProbity Mogul Percentile statistics Ideal geometry (proteins) Ideal geometry (DNA, RNA) Validation Pipeline (wwPDB-VP) : : : : : : 4.02b-467 unknown 20151230.v01 (using entries in the PDB archive December 30th 2015) Engh & Huber (2001) Parkinson et. al. (1996) rb-20027939 Page 2 1 wwPDB EM Map/Model Validation Report Overall quality at a glance O 3JBH i The following experimental techniques were used to determine the structure: ELECTRON MICROSCOPY The reported resolution of this entry is 20.00 Å. Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown in the following graphic. The table shows the number of entries on which the scores are based. Metric Clashscore Ramachandran outliers Sidechain outliers Whole archive (#Entries) 114402 111179 111093 EM structures (#Entries) 924 726 686 The table below summarises the geometric issues observed across the polymeric chains. The red, orange, yellow and green segments on the bar indicate the fraction of residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A grey segment represents the fraction of residues that are not modelled. The numeric value for each fraction is indicated below the corresponding segment, with a dot representing fractions <=5% Mol Chain Length 1 A 1953 1 B 1953 1 G 1953 1 H 1953 2 C 156 2 D 156 2 I 156 2 J 156 3 E 196 Quality of chain Continued on next page... Page 3 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Length 3 F 196 3 K 196 3 L 196 Quality of chain 3JBH Page 4 2 wwPDB EM Map/Model Validation Report Entry composition 3JBH O i There are 3 unique types of molecules in this entry. The entry contains 41968 atoms, of which 0 are hydrogens and 0 are deuteriums. In the tables below, the AltConf column contains the number of residues with at least one atom in alternate conformation and the Trace column contains the number of residues modelled with at most 2 atoms. Molecule 1 is a protein called MYOSIN 2 HEAVY CHAIN STRIATED MUSCLE. Mol Chain Residues 1 A 962 1 B 964 1 G 962 1 H 964 Total 7721 Total 7739 Total 7721 Total 7739 Atoms C 4907 C 4918 C 4907 C 4918 N 1334 N 1338 N 1334 N 1338 O 1450 O 1453 O 1450 O 1453 S 30 S 30 S 30 S 30 AltConf Trace 0 0 0 0 0 0 0 0 Molecule 2 is a protein called MYOSIN 2 ESSENTIAL LIGHT CHAIN STRIATED MUS- CLE. Mol Chain Residues 2 C 156 2 D 156 2 I 156 2 J 156 Total 1233 Total 1233 Total 1233 Total 1233 Atoms C 779 C 779 C 779 C 779 N 199 N 199 N 199 N 199 O 247 O 247 O 247 O 247 S 8 S 8 S 8 S 8 AltConf Trace 0 0 0 0 0 0 0 0 Molecule 3 is a protein called MYOSIN 2 REGULATORY LIGHT CHAIN STRIATED MUSCLE. Mol Chain Residues 3 E 196 3 F 196 3 K 196 3 L 196 Total 1529 Total 1529 Total 1529 Total 1529 Atoms C 952 C 952 C 952 C 952 N 257 N 257 N 257 N 257 O 314 O 314 O 314 O 314 S 6 S 6 S 6 S 6 AltConf Trace 0 0 0 0 0 0 0 0 ARG LEU THR VAL GLU ASN THR GLU LEU THR ARG GLN LEU GLU ASP ALA GLU SER GLN VAL SER GLN LEU SER LYS LEU LYS THR SER LEU GLN THR GLN LEU GLU ASP THR LYS ARG MET ALA ASP GLU GLU SER ARG GLU ARG ALA THR ALA MET GLY LYS PHE ARG SER VAL GLU HIS LYS GLU LYS ALA GLN MET LYS GLY GLU LEU ASP ASP VAL ARG SER SER VAL ASP HIS VAL ASN LYS GLU LYS ALA ASN ALA GLU LYS GLN ALA LYS GLN LEU GLU MET GLN LEU THR GLU LEU GLN GLY LYS MET ASP GLU ALA HIS ARG SER LEU GLY ASP PHE ASP ALA ALA LYS LYS ALA GLN VAL GLU LEU ASN LYS ARG ARG GLU ALA GLU MET ALA LYS LEU ARG ARG ASP LEU GLU GLU SER ASN ILE GLN HIS GLU GLN THR LEU ALA ASN LEU ARG LYS LYS HIS ASN ASP VAL VAL ALA GLU LEU SER GLU GLN ILE ASP GLN LEU ASN LYS HIS LYS ALA ARG LEU GLU GLY LEU VAL ALA LYS LEU GLN LYS GLN ILE LYS GLU LEU GLN ALA ARG ILE GLU GLU LEU GLU GLU GLU LEU GLU ALA GLU ARG GLN ALA ARG ALA LYS ALA GLU LYS GLN ARG ALA ASP LEU ALA ARG GLU ILE GLU GLU LEU SER GLU ARG LEU GLU GLU ALA GLY GLY ALA THR SER GLU ARG GLU LYS LYS LEU ARG GLY ASP VAL GLU LYS THR LYS ARG LYS VAL GLU GLY ASP LEU LYS LEU ALA GLN GLU ALA VAL ALA ASP LEU GLU LYS ASN LYS LYS GLU LEU GLU GLN ALA LEU GLN ARG LYS GLU LYS GLU MET ALA SER LEU SER ALA LYS LEU GLU ASP GLU GLN ASN ASP GLU ILE ALA HIS GLN ASP GLU LEU ILE ASN LYS LEU ASN ARG GLU LYS LYS GLN MET GLN GLU MET GLY GLN LYS THR GLY GLU ASP LEU GLN ALA THR GLU ASP LYS LEU ASN HIS MET ASN LYS VAL LYS ALA LYS LEU GLU GLN THR LEU ASP GLU LEU GLU ASP SER LEU I962 GLN LYS THR GLU GLN ASP LYS ALA ALA LYS ASP HIS GLN ILE ARG ASN LEU E947 D932 R929 N827 W828 L829 W830 Y831 K832 L833 Y834 I835 K836 V837 I815 R809 W792 I793 R794 W795 Y796 R778 D779 D780 R781 L782 G783 K784 I785 V786 T787 W788 L789 V770 L771 G772 R773 L774 E775 G760 N761 T762 K763 V764 F765 F766 R767 L482 A662 K543 H693 Q694 L695 T696 D719 F720 R708 K709 G710 F711 P712 N713 R714 M715 V716 K539 L690 P565 P566 K567 P568 G569 Q570 Q571 E572 V561 S557 P558 D547 W505 R673 C674 H665 S666 T667 Y498 K499 R500 E501 N479 R654 R640 N468 G469 F470 A460 G461 K447 Q448 K449 R450 Q451 Y452 R439 T409 Q410 G411 R412 E406 V397 K398 P399 L392 Y393 K394 N388 K360 F361 K362 Q363 R364 P365 R366 E367 E368 Q369 A370 E371 A372 D373 G374 T375 E376 E377 C353 D345 D334 D306 Y307 H308 F309 V310 S311 Q312 G313 R431 W435 L299 Q285 G423 M428 Y280 H281 I282 S272 V417 S418 Y419 S420 E629 D621 Q616 V603 V604 K596 D597 P598 V599 N600 W591 L592 E593 P585 Y586 N587 I588 F575 S576 E266 K267 A268 R269 V270 I271 A256 R240 D236 K231 T232 V118 A119 I120 N121 P122 N107 L108 I109 Y110 L100 K101 Q102 R103 L97 L88 G228 M85 P222 E80 Q72 Q61 E62 S63 R64 Q65 V66 I58 C54 T55 I46 Y41 E37 K38 W33 V34 K20 D21 Q22 Q17 L11 D6 P7 M1 P205 T206 K207 Y189 Y190 A191 N192 K185 E181 S175 G176 A177 L170 I171 T172 N166 Y157 H148 V145 Y137 K138 G139 R140 R141 R142 R132 T133 V134 Residue-property plots R926 E922 L923 L906 R896 L892 D887 Q883 E884 V879 R871 K872 D873 I874 E875 E867 E868 Y757 G735 F736 V737 Y724 K721 3 E854 M843 A844 K845 K838 P839 Page 5 wwPDB EM Map/Model Validation Report O 3JBH i These plots are drawn for all protein, RNA and DNA chains in the entry. The rst graphic for a chain summarises the proportions of errors displayed in the second graphic. The second graphic shows the sequence view annotated by issues in geometry. Residues are color-coded according to the number of geometric quality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretches of 2 or more consecutive residues without any outlier are shown as a green connector. Residues present in the sample, but not in the model, are shown in grey. • Molecule 1: MYOSIN 2 HEAVY CHAIN STRIATED MUSCLE Chain A: Q668 N658 R659 R654 G634 K635 G636 G637 G638 G639 R640 K641 K642 G643 A644 S645 F646 Q647 T648 A627 E628 E629 K630 I618 F619 E620 D621 H622 N612 K613 L614 K608 D601 W591 L592 E593 K594 N595 F575 P563 K564 P565 P566 K567 P568 Q546 D547 K548 E379 R380 F491 V492 L493 E494 Q495 E496 E497 Y498 K499 R500 E501 T541 E534 S535 M536 F537 C517 I518 E519 L520 I521 E522 K523 P524 M525 G526 I527 L528 S529 I530 L531 D504 W505 T375 H488 R439 W435 D430 R431 N413 A414 T415 Q416 V417 S418 Y419 S420 V421 G422 G423 L424 A425 K426 K400 I401 K402 V403 G404 N405 N388 A389 A390 D391 L392 Y393 E371 R364 P365 R366 E367 M354 H355 L356 G357 E341 Y342 K343 D330 T331 A332 E480 K481 E463 T446 K447 Q448 K449 R450 Q451 Y452 F453 I454 G455 V456 L440 N441 Y189 Y190 A191 N192 V193 P198 K199 P200 E203 A204 F283 F309 I315 Q312 D302 E292 G178 K179 T180 T172 G173 E174 S175 S168 M169 D154 G155 A156 Y157 S158 A159 M160 L161 A162 N163 R164 E165 R278 S279 Y280 Q274 T275 K267 A268 R269 V270 I271 I260 E261 T262 A256 P251 R240 F241 G242 K243 F244 I245 R246 I247 H248 V145 P146 P147 H148 L149 F150 A151 K138 G139 R140 R141 R142 A230 K231 T232 V233 R234 N235 D236 P222 R132 T133 V134 Y129 P122 Q219 K210 A211 P205 A119 Y112 L108 I109 R103 Y104 L97 L91 N92 D93 E83 D84 M85 S86 N87 V74 N75 P76 P77 K68 R64 Q65 D57 I58 C54 Y41 M31 V32 W33 Y26 K20 Y12 I13 S14 M1 A2 E3 D4 P5 D6 P7 T8 E9 MET GLY LYS PRO GLY ARG PRO LYS SER LYS ILE ASP GLU GLU LYS ARG GLN ILE GLU GLU ALA GLU GLU ILE ALA ALA LEU ASN LEU ALA LYS PHE ARG LYS VAL GLN GLN GLU LEU GLU ASP ALA GLU GLU ARG ALA ASP MET ALA GLU ASN VAL ALA ALA LYS LEU ARG ALA LYS ASN ARG SER SER ALA SER VAL GLY ARG ALA MET SER PRO ILE PRO VAL ARG GLU LEU GLU THR GLU LEU ASP ASN GLU GLN ARG ARG HIS SER GLU ALA ALA LYS ASN VAL ARG ARG SER GLU ARG ARG VAL LYS GLU LEU GLN PHE GLN ALA GLU GLU ASP ARG LYS ASN GLN GLU ARG MET GLN ASP LEU VAL ASP LYS LEU GLN GLN LYS ILE LYS THR TYR MET VAL ASP ALA ALA ARG LEU ALA ASP GLU LEU ARG ALA GLU GLN GLU HIS ALA GLN GLN GLN GLU LYS MET ARG LYS ALA MET GLU GLY GLN ILE LYS GLU LEU GLN VAL ARG LEU ASP GLU ALA GLU ALA ALA ALA LEU LYS GLY GLY LYS LYS ILE ILE GLN LYS LEU GLU GLN LYS ARG ARG ALA ALA ASP SER GLU LEU ALA GLU LEU HIS GLU ASN VAL ASN GLU LEU SER ALA GLN ASN SER SER LEU SER MET ALA LYS ARG LYS LEU GLU GLY GLU MET GLN ALA LEU HIS ALA ASP LEU ASP GLU MET LEU ASN GLU ALA LYS SER SER GLU GLU LYS ALA LYS LYS ALA ALA GLN LYS ASN ILE LYS LYS TYR GLN ILE GLN LEU LYS GLU THR GLN GLN ALA LEU GLU GLU GLU GLN ARG ALA ARG ASP GLU VAL ARG GLU GLN TYR ALA MET SER GLU ARG ARG CYS ASN ALA MET HIS GLY GLU LEU GLU GLU SER ARG GLN LEU LEU GLU GLN ALA ASP ARG ALA LYS GLU GLU GLU PHE GLU ASN THR ARG LYS ASN HIS GLN ARG ALA ILE ASP SER MET GLN ALA SER LEU GLU ALA GLU ALA LYS GLY LYS ALA GLU ALA LEU ARG MET LYS LYS LYS LEU GLU SER ASP ILE ASN GLU LEU GLU ILE ALA LEU ASP HIS SER ASN LYS ALA ASN ALA GLU GLY GLY ARG SER VAL HIS GLU LEU GLU LYS ALA ARG LYS ARG LEU GLU LEU GLU LYS GLU GLU LEU GLN ALA ALA LEU GLU GLU ALA GLU ALA ALA LEU GLU GLN GLU GLU ASN LYS VAL LEU ARG ALA GLN LEU GLU LEU SER GLN VAL ARG GLN GLU ILE ASP ARG ARG LEU GLN GLU LYS VAL ASP ASP LEU ALA LEU GLU LEU ASP ALA SER GLN LYS GLU CYS ARG ASN TYR SER THR GLU VAL PHE LYS LEU ARG SER GLN TYR GLU GLU SER GLN GLU HIS TYR GLU SER VAL LYS ARG GLU ASN LYS ASN LEU GLN ASP GLU ILE LYS ASP LEU VAL ASP GLN LEU GLY GLU GLU ALA MET GLU THR ILE ASP GLN LEU ASN SER LYS THR SER GLY LEU GLU LYS THR LYS SER ARG LEU GLN GLY GLU LEU GLU ASP MET THR ILE GLU VAL GLU LYS ALA ASN ALA LEU ALA SER ALA MET GLU LYS LYS GLN LYS SER PHE ASP ARG ILE ILE SER GLU TRP LYS GLN ASP LEU ASP SER LEU ARG GLU GLN ILE ASP GLU GLU GLN GLU GLY LYS ALA ASP LEU GLN ARG GLN LEU SER LYS ALA ASN ALA GLU VAL GLN LEU TRP ARG SER LYS TYR GLU SER GLU GLY LEU ALA ARG LEU GLU GLU LEU GLU GLU SER LYS ARG LYS LEU ASP ALA LYS LEU GLN Page 6 wwPDB EM Map/Model Validation Report 3JBH • Molecule 1: MYOSIN 2 HEAVY CHAIN STRIATED MUSCLE Chain B: THR GLU LEU ASP ASN GLU GLN ARG ARG HIS SER GLU ALA ALA LYS ASN VAL ARG ARG SER GLU ARG ARG VAL LYS GLU LEU GLN PHE GLN ALA GLU GLU ASP ARG LYS ASN GLN GLU ARG MET GLN ASP LEU VAL ASP LYS LEU GLN GLN LYS ILE LYS THR TYR LYS ARG GLN ILE GLU ARG LEU ALA ASP GLU LEU ARG ALA GLU GLN GLU HIS ALA GLN GLN GLN GLU LYS MET ARG LYS ALA MET GLU GLY GLN ILE LYS GLU LEU GLN VAL ARG LEU ASP GLU ALA GLU ALA ALA ALA LEU LYS GLY GLY LYS LYS ILE ILE GLN LYS LEU GLU GLN LYS VAL ARG GLU LEU GLU SER GLU LEU ALA GLU LEU HIS GLU ASN VAL ASN GLU LEU SER ALA GLN ASN SER SER LEU SER MET ALA LYS ARG LYS LEU GLU GLY GLU MET GLN ALA LEU HIS ALA ASP LEU ASP GLU MET LEU ASN GLU ALA LYS SER SER GLU GLU LYS ALA LYS LYS ALA MET VAL ASP ALA ALA LYS LYS TYR GLN ILE GLN LEU LYS GLU THR GLN GLN ALA LEU GLU GLU GLU GLN ARG ALA ARG ASP GLU VAL ARG GLU GLN TYR ALA MET SER GLU ARG ARG CYS ASN ALA MET HIS GLY GLU LEU GLU GLU SER ARG GLN LEU LEU GLU GLN ALA ASP ARG ALA ARG ARG ALA ALA ASP GLU ASN THR ARG LYS ASN HIS GLN ARG ALA ILE ASP SER MET GLN ALA SER LEU GLU ALA GLU ALA LYS GLY LYS ALA GLU ALA LEU ARG MET LYS LYS LYS LEU GLU SER ASP ILE ASN GLU LEU GLU ILE ALA LEU ASP HIS SER ASN LYS ALA ASN ALA GLU ALA GLN LYS ASN ILE HIS GLU LEU GLU LYS ALA ARG LYS ARG LEU GLU LEU GLU LYS GLU GLU LEU GLN ALA ALA LEU GLU GLU ALA GLU ALA ALA LEU GLU GLN GLU GLU ASN LYS VAL LEU ARG ALA GLN LEU GLU LEU SER GLN VAL ARG GLN GLU ILE ASP ARG ARG LEU GLN GLU LYS GLU GLU GLU PHE ALA LEU GLU LEU ASP ALA SER GLN LYS GLU CYS ARG ASN TYR SER THR GLU VAL PHE LYS LEU ARG SER GLN TYR GLU GLU SER GLN GLU HIS TYR GLU SER VAL LYS ARG GLU ASN LYS ASN LEU GLN ASP GLU ILE LYS ASP LEU VAL ASP GLN LEU GLY GLU GLY GLY ARG SER VAL ILE ASP GLN LEU ASN SER LYS THR SER GLY LEU GLU LYS THR LYS SER ARG LEU GLN GLY GLU LEU GLU ASP MET THR ILE GLU VAL GLU LYS ALA ASN ALA LEU ALA SER ALA MET GLU LYS LYS GLN LYS SER PHE ASP ARG ILE ILE SER GLU TRP LYS GLN LYS VAL ASP ASP LEU ARG GLU GLN ILE ASP GLU GLU GLN GLU GLY LYS ALA ASP LEU GLN ARG GLN LEU SER LYS ALA ASN ALA GLU VAL GLN LEU TRP ARG SER LYS TYR GLU SER GLU GLY LEU ALA ARG LEU GLU GLU LEU GLU GLU SER LYS ARG LYS LEU ASP ALA LYS LEU GLN GLU ALA MET GLU THR ASN THR GLU LEU THR ARG GLN LEU GLU ASP ALA GLU SER GLN VAL SER GLN LEU SER LYS LEU LYS THR SER LEU GLN THR GLN LEU GLU ASP THR LYS ARG MET ALA ASP GLU GLU SER ARG GLU ARG ALA THR ALA MET GLY LYS PHE ARG SER VAL GLU HIS ASP LEU ASP SER LEU MET LYS GLY GLU LEU ASP ASP VAL ARG SER SER VAL ASP HIS VAL ASN LYS GLU LYS ALA ASN ALA GLU LYS GLN ALA LYS GLN LEU GLU MET GLN LEU THR GLU LEU GLN GLY LYS MET ASP GLU ALA HIS ARG SER LEU GLY ASP PHE ASP ALA ALA LYS LYS ARG LEU THR VAL GLU ASN LYS ARG ARG GLU ALA GLU MET ALA LYS LEU ARG ARG ASP LEU GLU GLU SER ASN ILE GLN HIS GLU GLN THR LEU ALA ASN LEU ARG LYS LYS HIS ASN ASP VAL VAL ALA GLU LEU SER GLU GLN ILE ASP GLN LEU ASN LYS HIS LYS ALA ARG LEU GLU LYS GLU LYS ALA GLN LEU GLN LYS GLN ILE LYS GLU LEU GLN ALA ARG ILE GLU GLU LEU GLU GLU GLU LEU GLU ALA GLU ARG GLN ALA ARG ALA LYS ALA GLU LYS GLN ARG ALA ASP LEU ALA ARG GLU ILE GLU GLU LEU SER GLU ARG LEU GLU GLU ALA GLY GLY ALA THR SER ALA GLN VAL GLU LEU LEU ARG GLY ASP VAL GLU LYS THR LYS ARG LYS VAL GLU GLY ASP LEU LYS LEU ALA GLN GLU ALA VAL ALA ASP LEU GLU LYS ASN LYS LYS GLU LEU GLU GLN ALA LEU GLN ARG LYS GLU LYS GLU MET ALA SER LEU SER ALA LYS LEU GLU ASP GLU GLN GLY LEU VAL ALA LYS HIS GLN ASP GLU LEU ILE ASN LYS LEU ASN ARG GLU LYS LYS GLN MET GLN GLU MET GLY GLN LYS THR GLY GLU ASP LEU GLN ALA THR GLU ASP LYS LEU ASN HIS MET ASN LYS VAL LYS ALA LYS LEU GLU GLN THR LEU ASP GLU LEU GLU ASP SER LEU GLU ARG GLU LYS LYS K964 THR GLU GLN ASP LYS ALA ALA LYS ASP HIS GLN ILE ARG ASN LEU ASN ASP GLU ILE ALA D957 K953 E954 I948 R941 A933 R929 E930 Q924 E925 R926 V902 E903 E904 R905 L906 T907 K908 R896 D887 N878 V870 R871 K872 D873 I874 E875 R758 N761 T762 K763 E867 E868 K869 I750 Q751 L752 K740 K741 V742 T743 E744 A745 V746 V732 P733 K734 K721 Q722 R723 Y724 T725 I726 L727 F711 P712 N713 R714 M715 V716 Y717 P718 R708 R705 L701 E702 M692 I686 L680 K681 R673 C674 I675 I676 P669 H670 E862 S863 L864 T842 M843 A844 K845 V846 E847 D848 R826 N827 W828 L829 W830 Y831 K832 L833 Y834 I835 K836 V837 K838 R817 R809 V810 A811 K804 W788 L789 Q790 A791 W792 I793 R794 W795 I785 L782 D779 E776 G769 V770 L771 V764 Page 7 wwPDB EM Map/Model Validation Report 3JBH ILE ASP GLU GLU GLN GLU GLY LYS ALA ASP LEU GLN ARG GLN LEU SER LYS ALA ASN ALA GLU VAL GLN LEU TRP ARG SER LYS TYR GLU SER GLU GLY LEU ALA ARG LEU GLU GLU LEU GLU GLU SER LYS ARG LYS LEU ASP ALA LYS LEU GLN GLU ALA MET GLU THR ILE ASP GLN LEU THR ARG GLN LEU GLU ASP ALA GLU SER GLN VAL SER GLN LEU SER LYS LEU LYS THR SER LEU GLN THR GLN LEU GLU ASP THR LYS ARG MET ALA ASP GLU GLU SER ARG GLU ARG ALA THR ALA MET GLY LYS PHE ARG SER VAL GLU HIS ASP LEU ASP SER LEU ARG GLU GLN GLU LEU ASP ASP VAL ARG SER SER VAL ASP HIS VAL ASN LYS GLU LYS ALA ASN ALA GLU LYS GLN ALA LYS GLN LEU GLU MET GLN LEU THR GLU LEU GLN GLY LYS MET ASP GLU ALA HIS ARG SER LEU GLY ASP PHE ASP ALA ALA LYS LYS ARG LEU THR VAL GLU ASN THR GLU ARG GLU ALA GLU MET ALA LYS LEU ARG ARG ASP LEU GLU GLU SER ASN ILE GLN HIS GLU GLN THR LEU ALA ASN LEU ARG LYS LYS HIS ASN ASP VAL VAL ALA GLU LEU SER GLU GLN ILE ASP GLN LEU ASN LYS HIS LYS ALA ARG LEU GLU LYS GLU LYS ALA GLN MET LYS GLY GLN ILE LYS GLU LEU GLN ALA ARG ILE GLU GLU LEU GLU GLU GLU LEU GLU ALA GLU ARG GLN ALA ARG ALA LYS ALA GLU LYS GLN ARG ALA ASP LEU ALA ARG GLU ILE GLU GLU LEU SER GLU ARG LEU GLU GLU ALA GLY GLY ALA THR SER ALA GLN VAL GLU LEU ASN LYS ARG ASP VAL GLU LYS THR LYS ARG LYS VAL GLU GLY ASP LEU LYS LEU ALA GLN GLU ALA VAL ALA ASP LEU GLU LYS ASN LYS LYS GLU LEU GLU GLN ALA LEU GLN ARG LYS GLU LYS GLU MET ALA SER LEU SER ALA LYS LEU GLU ASP GLU GLN GLY LEU VAL ALA LYS LEU GLN LYS GLU LEU ILE ASN LYS LEU ASN ARG GLU LYS LYS GLN MET GLN GLU MET GLY GLN LYS THR GLY GLU ASP LEU GLN ALA THR GLU ASP LYS LEU ASN HIS MET ASN LYS VAL LYS ALA LYS LEU GLU GLN THR LEU ASP GLU LEU GLU ASP SER LEU GLU ARG GLU LYS LYS LEU ARG GLY I962 GLN LYS THR GLU GLN ASP LYS ALA ALA LYS ASP HIS GLN ILE ARG ASN LEU ASN ASP GLU ILE ALA HIS GLN ASP L951 R926 E922 L923 Q919 E904 R905 L906 D901 R896 D887 L888 F889 L890 Q891 L892 Q883 E884 S863 L864 E865 K866 E867 E854 M843 V837 K838 P839 N827 W828 L829 W830 Y831 K832 L833 R820 I815 Q816 R817 R809 A791 W792 I793 R794 W795 L782 G783 K784 I785 V786 T787 W788 R778 D779 R773 G760 N761 T762 K763 V764 F765 F766 R767 A768 G769 D756 Y757 V746 T743 M490 F491 V492 R640 G735 F736 V737 Y724 K721 G710 F711 P712 N713 R714 M715 V716 Y717 P718 R705 L701 E702 D345 V346 Y347 M354 N468 G469 F470 C474 Q616 L326 R327 D334 Y305 D306 Y307 H308 F309 V310 S311 Q312 G313 L298 L299 L300 S301 Q285 L286 M287 I282 E277 G228 E225 T220 N221 P222 D215 Q216 V217 T212 A204 P205 T206 K207 A195 A196 T197 Y189 Y190 A177 E174 R164 E165 N166 Y157 A151 Y137 K138 G139 R140 R141 R142 T143 E144 I260 L264 L265 E266 K267 A268 R269 V270 I271 S272 Q273 Y26 V134 A256 N107 L108 I109 L100 K101 Q102 L97 L91 N92 D93 N87 D84 E80 V74 R64 Q65 V66 Q61 C54 T55 V56 D57 I58 I46 Y41 E37 K38 W33 V34 Q17 K20 D21 Q22 E9 Y10 L11 D4 M1 N131 V118 A119 I120 N121 P122 Y123 G114 L115 K243 F244 I245 R246 D236 N237 S238 T232 D458 I459 A460 R450 Q451 Y452 K447 R439 W435 R431 S418 Y419 S420 V421 G422 G423 L424 A425 K426 Q410 G411 D391 L392 Y393 V381 T375 E376 E377 G378 A372 R366 E367 E368 Q369 E358 M359 K360 F361 K362 H355 K596 D597 P598 V599 N600 D601 T602 V603 V604 D605 W591 L592 E593 P585 Y586 N587 I588 F575 S576 Q571 E572 L695 P568 V691 V561 D547 K548 L549 K543 P538 I527 A516 W505 S688 Q682 P683 R673 C674 I675 I676 H665 S666 T667 Q668 P669 R659 L660 M661 R654 E497 Y498 K499 R500 E501 F486 E629 S645 F646 Q647 Q483 D621 ARG PRO LYS SER LYS ILE ASP GLU GLU GLU ALA GLU GLU ILE ALA ALA LEU ASN LEU ALA LYS PHE ARG LYS VAL GLN GLN GLU LEU GLU ASP ALA GLU GLU ARG ALA ASP MET ALA GLU ASN VAL ALA ALA LYS LEU ARG ALA LYS ASN ARG SER SER ALA SER VAL GLY ARG ALA MET SER PRO ILE PRO MET GLY LYS PRO GLY Page 8 wwPDB EM Map/Model Validation Report 3JBH • Molecule 1: MYOSIN 2 HEAVY CHAIN STRIATED MUSCLE Chain G: V742 T743 D738 V732 P733 K721 Q722 R723 Y724 T725 I726 F711 P712 N713 R714 M715 V716 R705 I706 C707 L701 E702 L695 I686 L680 K681 V672 R673 C674 I675 I676 P677 T667 Q668 R659 R654 K641 K642 G643 A644 S645 F646 Q647 T648 V649 D330 T331 R439 E480 K481 L482 Q483 Q484 F491 V492 L493 I588 D597 P598 V599 N600 D601 K635 G636 G637 G638 G639 R640 A627 E628 E629 K630 G631 G632 I618 F619 E620 D621 H622 K613 Q606 F607 K608 T541 D542 K543 L528 S529 I530 I521 E522 K523 P524 I518 G511 L512 I503 D504 W505 E496 E497 Y498 K499 R500 L473 Y580 W591 L592 E593 F462 E463 R450 Q451 Y452 F453 I454 G455 V456 L457 Y419 S420 V421 G422 G423 L424 A425 K426 R412 N405 K400 I401 K402 V397 A389 L384 R380 T375 E376 E377 E371 R364 P365 R366 E367 M354 H355 L356 G357 E358 E341 Y342 K343 T344 D345 V346 Y347 D334 I315 W435 T446 Y307 D430 R431 Q571 E572 A573 H574 F575 S576 V561 K562 P563 K564 P565 P566 K567 S544 F545 Q546 D547 K548 L298 L299 L300 S301 D302 K295 R278 S279 Y280 H281 I282 F283 L265 E266 K267 A258 D259 I260 F244 I245 R246 I247 H248 F249 G250 P251 R240 R234 N235 D236 N237 K231 P222 Q219 E214 D215 K210 A211 A119 I120 E203 A204 P205 T206 K207 T197 R103 L108 I109 Y110 T111 L97 Y190 A191 N192 V193 Y90 L91 N92 D93 Y79 E80 K81 C82 E83 D84 M85 S86 Q72 K68 R64 C54 T55 V56 D57 I58 W33 Y26 D27 G28 L11 Y12 I13 S14 M15 E16 Q17 K18 R19 K20 D21 M1 A2 E3 D4 P5 D6 P7 K185 G178 K179 T180 S175 A162 N163 R164 E165 N166 Q167 S168 M169 L170 I171 Y157 S158 A159 A151 N131 R132 T133 V134 Q135 I136 Y137 K138 G139 R140 R141 R142 T143 E144 V145 P146 P147 F126 P127 I128 Y112 S113 G114 P198 K199 P200 SER LYS ILE ASP GLU GLU GLU ILE ALA ALA LEU ASN LEU ALA LYS PHE ARG LYS VAL GLN GLN GLU LEU GLU ASP ALA GLU GLU ARG ALA ASP MET ALA GLU ASN VAL ALA ALA LYS LEU ARG ALA LYS ASN ARG SER SER ALA SER VAL GLY ARG ALA MET SER PRO ILE PRO MET GLY LYS PRO GLY ARG PRO LYS ASP ASN GLU GLN ARG ARG HIS SER GLU ALA ALA LYS ASN VAL ARG ARG SER GLU ARG ARG VAL LYS GLU LEU GLN PHE GLN ALA GLU GLU ASP ARG LYS ASN GLN GLU ARG MET GLN ASP LEU VAL ASP LYS LEU GLN GLN LYS ILE LYS THR TYR LYS ARG GLN ILE GLU GLU ALA GLU ASP GLU LEU ARG ALA GLU GLN GLU HIS ALA GLN GLN GLN GLU LYS MET ARG LYS ALA MET GLU GLY GLN ILE LYS GLU LEU GLN VAL ARG LEU ASP GLU ALA GLU ALA ALA ALA LEU LYS GLY GLY LYS LYS ILE ILE GLN LYS LEU GLU GLN LYS VAL ARG GLU LEU GLU THR GLU LEU ALA GLU LEU HIS GLU ASN VAL ASN GLU LEU SER ALA GLN ASN SER SER LEU SER MET ALA LYS ARG LYS LEU GLU GLY GLU MET GLN ALA LEU HIS ALA ASP LEU ASP GLU MET LEU ASN GLU ALA LYS SER SER GLU GLU LYS ALA LYS LYS ALA MET VAL ASP ALA ALA ARG LEU ALA GLN ILE GLN LEU LYS GLU THR GLN GLN ALA LEU GLU GLU GLU GLN ARG ALA ARG ASP GLU VAL ARG GLU GLN TYR ALA MET SER GLU ARG ARG CYS ASN ALA MET HIS GLY GLU LEU GLU GLU SER ARG GLN LEU LEU GLU GLN ALA ASP ARG ALA ARG ARG ALA ALA ASP SER GLU LEU ARG LYS ASN HIS GLN ARG ALA ILE ASP SER MET GLN ALA SER LEU GLU ALA GLU ALA LYS GLY LYS ALA GLU ALA LEU ARG MET LYS LYS LYS LEU GLU SER ASP ILE ASN GLU LEU GLU ILE ALA LEU ASP HIS SER ASN LYS ALA ASN ALA GLU ALA GLN LYS ASN ILE LYS LYS TYR GLU LYS ALA ARG LYS ARG LEU GLU LEU GLU LYS GLU GLU LEU GLN ALA ALA LEU GLU GLU ALA GLU ALA ALA LEU GLU GLN GLU GLU ASN LYS VAL LEU ARG ALA GLN LEU GLU LEU SER GLN VAL ARG GLN GLU ILE ASP ARG ARG LEU GLN GLU LYS GLU GLU GLU PHE GLU ASN THR LEU ASP ALA SER GLN LYS GLU CYS ARG ASN TYR SER THR GLU VAL PHE LYS LEU ARG SER GLN TYR GLU GLU SER GLN GLU HIS TYR GLU SER VAL LYS ARG GLU ASN LYS ASN LEU GLN ASP GLU ILE LYS ASP LEU VAL ASP GLN LEU GLY GLU GLY GLY ARG SER VAL HIS GLU LEU LEU ASN SER LYS THR SER GLY LEU GLU LYS THR LYS SER ARG LEU GLN GLY GLU LEU GLU ASP MET THR ILE GLU VAL GLU LYS ALA ASN ALA LEU ALA SER ALA MET GLU LYS LYS GLN LYS SER PHE ASP ARG ILE ILE SER GLU TRP LYS GLN LYS VAL ASP ASP LEU ALA LEU GLU Page 9 wwPDB EM Map/Model Validation Report 3JBH • Molecule 1: MYOSIN 2 HEAVY CHAIN STRIATED MUSCLE Chain H: GLU ILE ALA ALA LEU ASN LEU ALA LYS PHE ARG LYS VAL GLN GLN GLU LEU GLU ASP ALA GLU GLU ARG ALA ASP MET ALA GLU ASN VAL ALA ALA LYS LEU ARG ALA LYS ASN ARG SER SER ALA SER VAL GLY ARG ALA MET SER PRO ILE PRO MET GLY LYS PRO GLY ARG PRO LYS ASP ASN GLU GLN ARG ARG HIS SER GLU ALA ALA LYS ASN VAL ARG ARG SER GLU ARG ARG VAL LYS GLU LEU GLN PHE GLN ALA GLU GLU ASP ARG LYS ASN GLN GLU ARG MET GLN ASP LEU VAL ASP LYS LEU GLN GLN LYS ILE LYS THR TYR LYS ARG GLN ILE GLU GLU ALA GLU ASP GLU LEU ARG ALA GLU GLN GLU HIS ALA GLN GLN GLN GLU LYS MET ARG LYS ALA MET GLU GLY GLN ILE LYS GLU LEU GLN VAL ARG LEU ASP GLU ALA GLU ALA ALA ALA LEU LYS GLY GLY LYS LYS ILE ILE GLN LYS LEU GLU GLN LYS VAL ARG GLU LEU GLU THR GLU LEU ALA GLU LEU HIS GLU ASN VAL ASN GLU LEU SER ALA GLN ASN SER SER LEU SER MET ALA LYS ARG LYS LEU GLU GLY GLU MET GLN ALA LEU HIS ALA ASP LEU ASP GLU MET LEU ASN GLU ALA LYS SER SER GLU GLU LYS ALA LYS LYS ALA MET VAL ASP ALA ALA ARG LEU ALA GLN ILE GLN LEU LYS GLU THR GLN GLN ALA LEU GLU GLU GLU GLN ARG ALA ARG ASP GLU VAL ARG GLU GLN TYR ALA MET SER GLU ARG ARG CYS ASN ALA MET HIS GLY GLU LEU GLU GLU SER ARG GLN LEU LEU GLU GLN ALA ASP ARG ALA ARG ARG ALA ALA ASP SER GLU LEU ARG LYS ASN HIS GLN ARG ALA ILE ASP SER MET GLN ALA SER LEU GLU ALA GLU ALA LYS GLY LYS ALA GLU ALA LEU ARG MET LYS LYS LYS LEU GLU SER ASP ILE ASN GLU LEU GLU ILE ALA LEU ASP HIS SER ASN LYS ALA ASN ALA GLU ALA GLN LYS ASN ILE LYS LYS TYR GLU LYS ALA ARG LYS ARG LEU GLU LEU GLU LYS GLU GLU LEU GLN ALA ALA LEU GLU GLU ALA GLU ALA ALA LEU GLU GLN GLU GLU ASN LYS VAL LEU ARG ALA GLN LEU GLU LEU SER GLN VAL ARG GLN GLU ILE ASP ARG ARG LEU GLN GLU LYS GLU GLU GLU PHE GLU ASN THR LEU ASP ALA SER GLN LYS GLU CYS ARG ASN TYR SER THR GLU VAL PHE LYS LEU ARG SER GLN TYR GLU GLU SER GLN GLU HIS TYR GLU SER VAL LYS ARG GLU ASN LYS ASN LEU GLN ASP GLU ILE LYS ASP LEU VAL ASP GLN LEU GLY GLU GLY GLY ARG SER VAL HIS GLU LEU LEU ASN SER LYS THR SER GLY LEU GLU LYS THR LYS SER ARG LEU GLN GLY GLU LEU GLU ASP MET THR ILE GLU VAL GLU LYS ALA ASN ALA LEU ALA SER ALA MET GLU LYS LYS GLN LYS SER PHE ASP ARG ILE ILE SER GLU TRP LYS GLN LYS VAL ASP ASP LEU ALA LEU GLU ILE ASP GLU GLU GLN GLU GLY LYS ALA ASP LEU GLN ARG GLN LEU SER LYS ALA ASN ALA GLU VAL GLN LEU TRP ARG SER LYS TYR GLU SER GLU GLY LEU ALA ARG LEU GLU GLU LEU GLU GLU SER LYS ARG LYS LEU ASP ALA LYS LEU GLN GLU ALA MET GLU THR ILE ASP GLN LEU THR ARG GLN LEU GLU ASP ALA GLU SER GLN VAL SER GLN LEU SER LYS LEU LYS THR SER LEU GLN THR GLN LEU GLU ASP THR LYS ARG MET ALA ASP GLU GLU SER ARG GLU ARG ALA THR ALA MET GLY LYS PHE ARG SER VAL GLU HIS ASP LEU ASP SER LEU ARG GLU GLN GLU LEU ASP ASP VAL ARG SER SER VAL ASP HIS VAL ASN LYS GLU LYS ALA ASN ALA GLU LYS GLN ALA LYS GLN LEU GLU MET GLN LEU THR GLU LEU GLN GLY LYS MET ASP GLU ALA HIS ARG SER LEU GLY ASP PHE ASP ALA ALA LYS LYS ARG LEU THR VAL GLU ASN THR GLU ARG GLU ALA GLU MET ALA LYS LEU ARG ARG ASP LEU GLU GLU SER ASN ILE GLN HIS GLU GLN THR LEU ALA ASN LEU ARG LYS LYS HIS ASN ASP VAL VAL ALA GLU LEU SER GLU GLN ILE ASP GLN LEU ASN LYS HIS LYS ALA ARG LEU GLU LYS GLU LYS ALA GLN MET LYS GLY GLN ILE LYS GLU LEU GLN ALA ARG ILE GLU GLU LEU GLU GLU GLU LEU GLU ALA GLU ARG GLN ALA ARG ALA LYS ALA GLU LYS GLN ARG ALA ASP LEU ALA ARG GLU ILE GLU GLU LEU SER GLU ARG LEU GLU GLU ALA GLY GLY ALA THR SER ALA GLN VAL GLU LEU ASN LYS ARG ASP VAL GLU LYS THR LYS ARG LYS VAL GLU GLY ASP LEU LYS LEU ALA GLN GLU ALA VAL ALA ASP LEU GLU LYS ASN LYS LYS GLU LEU GLU GLN ALA LEU GLN ARG LYS GLU LYS GLU MET ALA SER LEU SER ALA LYS LEU GLU ASP GLU GLN GLY LEU VAL ALA LYS LEU GLN LYS GLU LEU ILE ASN LYS LEU ASN ARG GLU LYS LYS GLN MET GLN GLU MET GLY GLN LYS THR GLY GLU ASP LEU GLN ALA THR GLU ASP LYS LEU ASN HIS MET ASN LYS VAL LYS ALA LYS LEU GLU GLN THR LEU ASP GLU LEU GLU ASP SER LEU GLU ARG GLU LYS LYS LEU ARG GLY W788 W792 I793 R794 W795 Y796 K803 K804 R941 I948 D957 K964 THR GLU GLN ASP LYS ALA ALA LYS ASP HIS GLN ILE ARG ASN LEU ASN ASP GLU ILE ALA HIS GLN ASP T842 M843 A844 K845 R826 N827 W828 L829 W830 Y831 K832 L833 Y834 I835 K836 V837 K838 R817 R809 I785 A933 K952 K953 E954 D779 E776 R767 A768 G769 V770 L771 G772 R773 K763 V764 G760 I750 Q751 L752 V746 L747 R929 E930 L923 Q924 E925 L906 S894 E895 R896 S897 D887 R871 E868 E862 D848 Page 10 wwPDB EM Map/Model Validation Report 3JBH R88 L89 C90 D78 I79 R80 A81 T82 K60 E61 A62 F63 Q64 L65 I66 D67 Q68 D69 K70 D71 G72 F73 T52 Q53 H54 Q55 V56 Q57 R42 P28 P29 P30 P31 K32 P33 P34 K9 K10 K11 K12 S13 K14 K15 K16 S17 E18 E19 E20 G21 G22 M1 G2 D3 A191 E192 E193 E194 G195 A196 E169 K157 T153 W154 I106 N107 F108 E94 L89 C90 L86 F83 D78 I79 R80 K70 D71 G72 F73 I74 D67 M50 F51 T52 Q53 H54 Q55 V56 Q57 E58 F59 N46 V47 S43 P33 P34 S35 Q36 K37 P28 P29 P30 S17 E18 E19 E20 G21 E5 R118 G138 E139 G140 M1 T109 K156 D153 P152 I147 F136 L137 K138 Y139 E140 P141 D130 E131 D119 R116 L111 S112 M101 V92 Y93 D94 L83 E84 D85 K75 E66 F67 L68 P69 K60 K61 L62 T63 R37 R30 K26 I27 W21 E22 R13 M1 A2 D3 L4 K5 K156 P152 I146 V143 F136 L137 K138 Y139 E140 E131 I125 D119 R116 T100 M101 L102 A103 E97 Y93 D94 L90 N51 D40 C41 K42 P43 T44 R37 W21 R13 M1 K156 P152 I147 Y139 E140 P141 D134 G135 D130 R127 D119 L111 S112 V92 Y93 D94 L83 E84 D85 K61 R57 D40 C41 K42 P43 R37 D34 Y19 D20 W21 E22 R13 M1 K156 P152 I147 K138 Y139 E140 P141 D133 R116 L90 K91 V92 Y93 D94 K95 A96 E97 P69 N51 G52 G53 V48 C41 R37 W21 R13 M1 SER LYS ILE ASP GLU GLU Page 11 wwPDB EM Map/Model Validation Report 3JBH • Molecule 2: MYOSIN 2 ESSENTIAL LIGHT CHAIN STRIATED MUSCLE Chain C: • Molecule 2: MYOSIN 2 ESSENTIAL LIGHT CHAIN STRIATED MUSCLE Chain D: • Molecule 2: MYOSIN 2 ESSENTIAL LIGHT CHAIN STRIATED MUSCLE Chain I: • Molecule 2: MYOSIN 2 ESSENTIAL LIGHT CHAIN STRIATED MUSCLE Chain J: • Molecule 3: MYOSIN 2 REGULATORY LIGHT CHAIN STRIATED MUSCLE Chain E: • Molecule 3: MYOSIN 2 REGULATORY LIGHT CHAIN STRIATED MUSCLE Chain F: T188 K189 G190 A191 E192 E193 E194 G195 A196 I178 D173 G174 W154 K141 C142 K143 E144 I128 V129 N130 A131 F132 N133 L134 D123 E124 E125 T113 I106 C90 T91 E92 Q93 E94 L95 D96 S97 M98 V99 A100 E101 A102 P103 L89 S85 I79 R80 D67 Q68 D69 K70 D71 G72 F73 E58 F59 K60 E61 A62 F63 Q53 H54 Q55 S45 R42 R39 P29 P30 P31 K32 P33 P34 S35 Q36 G22 D23 K9 K10 K11 K12 S13 K14 K15 K16 S17 E18 K6 M1 G2 D3 E5 K16 S17 F183 G190 A191 E192 E193 E194 G195 A196 W154 R149 G138 E139 G140 R118 G104 P105 I106 N107 F108 T109 L86 G87 D78 I79 R80 I74 K70 D67 F51 T52 Q53 H54 Q55 V56 Q57 E58 F59 Q41 R42 R38 P33 P34 P29 E20 G21 M1 E169 T188 K189 G190 A191 E192 E193 E194 G195 A196 I178 D173 G174 S168 W154 K141 C142 K143 E144 N130 A131 F132 D123 E124 E125 D126 V127 D117 R118 I119 A120 T113 P105 V99 E94 L95 Page 12 wwPDB EM Map/Model Validation Report 3JBH • Molecule 3: MYOSIN 2 REGULATORY LIGHT CHAIN STRIATED MUSCLE Chain K: • Molecule 3: MYOSIN 2 REGULATORY LIGHT CHAIN STRIATED MUSCLE Chain L: Page 13 4 wwPDB EM Map/Model Validation Report Experimental information Property Reconstruction method Imposed symmetry Number of segments used Resolution determination method CTF correction method Microscope Voltage (kV) 2 Electron dose (e− /Å ) Minimum defocus (nm) Maximum defocus (nm) Magnication Image detector Value 3JBH O i HELICAL POINT, Not provided Not provided FSC 0.5 Not provided FEI/PHILIPS CM120T 120 Not provided 1950 1950 35000 KODAK SO-163 FILM Source Depositor Depositor Depositor Depositor Depositor Depositor Depositor Depositor Depositor Depositor Depositor Depositor Page 14 5 wwPDB EM Map/Model Validation Report Model quality 5.1 O 3JBH i Standard geometry O i The Z score for a bond length (or angle) is the number of standard deviations the observed value is removed from the expected value. A bond length (or angle) with |Z| > 5 is considered an outlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles). Bond lengths Mol Chain RMSZ #|Z| >2 1 1 1 1 2 2 2 2 3 3 3 3 All A B G H C D I J E F K L All 0.65 0.64 0.64 0.64 0.66 0.66 0.64 0.65 0.64 0.64 0.65 0.69 0.65 0/7867 0/7885 0/7867 0/7885 0/1251 0/1251 0/1251 0/1251 0/1554 0/1554 0/1554 0/1554 0/42724 Bond angles RMSZ #|Z| >2 1.36 93/10591 (0.9%) 1.35 68/10614 (0.6%) 1.33 75/10591 (0.7%) 1.34 64/10614 (0.6%) 1.20 6/1674 (0.4%) 1.19 8/1674 (0.5%) 1.21 9/1674 (0.5%) 1.21 7/1674 (0.4%) 1.20 10/2081 (0.5%) 1.30 11/2081 (0.5%) 1.24 9/2081 (0.4%) 1.40 17/2081 (0.8%) 1.32 377/57430 (0.7%) Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying if the center is modelled as a planar moiety or with the opposite hand. A planarity outlier is detected by checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of a sidechain that are expected to be planar. Mol Chain #Chirality outliers #Planarity outliers 1 1 1 1 2 2 2 3 3 3 3 All A B G H D I J E F K L All 0 0 0 0 0 0 0 0 0 0 0 0 32 20 25 19 1 1 4 1 3 2 8 116 Page 15 wwPDB EM Map/Model Validation Report 3JBH There are no bond length outliers. All (377) bond angle outliers are listed below: Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 3 1 1 1 1 1 2 1 1 1 1 1 1 3 3 1 1 1 3 1 A B G B G G H G G A B L H A H A A B A G E B A G G H C B G A A H B L K G A A L H 365 380 140 654 367 367 64 64 778 367 12 39 929 367 364 364 365 439 140 310 154 929 505 505 310 654 21 140 788 306 591 929 794 13 118 206 788 362 154 828 PRO ARG ARG ARG GLU GLU ARG ARG ARG GLU TYR ARG ARG GLU ARG ARG PRO ARG ARG VAL TRP ARG TRP TRP VAL ARG TRP ARG TRP ASP TRP ARG ARG SER ARG THR TRP LYS TRP TRP Atoms CA-N-CD NE-CZ-NH1 NE-CZ-NH1 NE-CZ-NH1 CA-C-N O-C-N NE-CZ-NH1 NE-CZ-NH1 NE-CZ-NH1 CA-C-N CB-CG-CD2 NE-CZ-NH1 NE-CZ-NH1 O-C-N NE-CZ-NH1 NE-CZ-NH1 N-CA-C NE-CZ-NH1 NE-CZ-NH1 CA-C-N CD1-CG-CD2 NE-CZ-NH1 CD1-CG-CD2 CD1-CG-CD2 O-C-N NE-CZ-NH1 CD1-CG-CD2 NE-CZ-NH1 CD1-CG-CD2 N-CA-C CD1-CG-CD2 NE-CZ-NH2 NE-CZ-NH1 O-C-N NE-CZ-NH1 CA-C-N CD1-CG-CD2 C-N-CA CD1-CG-CD2 CD1-CG-CD2 Z -13.39 -12.71 -10.79 -10.67 10.62 -10.30 -10.23 -10.13 -9.87 9.85 -9.84 -9.62 -9.50 -9.49 -9.40 9.19 9.18 -9.11 -9.09 9.03 9.02 -8.99 8.94 8.93 -8.91 -8.85 8.84 -8.79 8.72 8.62 8.57 8.57 -8.56 -8.55 -8.52 8.49 8.48 8.46 8.46 8.44 Observed( ) Ideal( ) o 92.75 113.94 114.91 114.97 140.56 106.22 115.18 115.24 115.36 138.87 115.10 115.49 115.55 107.52 115.60 124.89 135.98 115.74 115.76 137.06 113.51 115.80 113.45 113.44 108.45 115.87 113.37 115.91 113.28 134.27 113.16 124.58 116.02 109.02 116.04 135.87 113.08 142.85 113.07 113.05 o 111.50 120.30 120.30 120.30 117.20 122.70 120.30 120.30 120.30 117.20 121.00 120.30 120.30 122.70 120.30 120.30 112.10 120.30 120.30 117.20 106.30 120.30 106.30 106.30 122.70 120.30 106.30 120.30 106.30 111.00 106.30 120.30 120.30 122.70 120.30 117.20 106.30 121.70 106.30 106.30 Continued on next page... Page 16 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 2 1 1 3 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 2 3 2 1 1 3 1 1 1 1 1 1 2 1 1 I H B E A A J H A B A B H B G G G H G H B A B E A A H I K C H G F B A H G G H C A G 21 565 830 118 778 788 13 830 505 103 206 795 500 565 505 788 673 788 591 591 640 828 828 154 828 435 64 37 154 21 830 435 154 33 311 795 140 568 33 13 33 206 TRP PRO TRP ARG ARG TRP ARG TRP TRP ARG THR TRP ARG PRO TRP TRP ARG TRP TRP TRP ARG TRP TRP TRP TRP TRP ARG ARG TRP TRP TRP TRP TRP TRP SER TRP ARG PRO TRP ARG TRP THR Atoms CD1-CG-CD2 N-CA-C CD1-CG-CD2 NE-CZ-NH2 NE-CZ-NH1 CE2-CD2-CG NE-CZ-NH1 CD1-CG-CD2 CE2-CD2-CG NE-CZ-NH2 CA-C-N CD1-CG-CD2 NE-CZ-NH2 N-CA-C CE2-CD2-CG CE2-CD2-CG NE-CZ-NH1 CD1-CG-CD2 CD1-CG-CD2 CD1-CG-CD2 NE-CZ-NH2 CD1-CG-CD2 CD1-CG-CD2 CE2-CD2-CG CE2-CD2-CG CD1-CG-CD2 NE-CZ-NH2 NE-CZ-NH1 CD1-CG-CD2 CE2-CD2-CG CE2-CD2-CG CD1-CG-CD2 CD1-CG-CD2 CE2-CD2-CG N-CA-C CD1-CG-CD2 NE-CZ-NH2 CA-N-CD CD1-CG-CD2 NE-CZ-NH2 CD1-CG-CD2 O-C-N Z 8.43 8.39 8.38 8.36 -8.35 -8.33 -8.33 8.32 -8.26 8.21 8.20 8.19 8.18 8.17 -8.14 -8.13 -8.11 8.11 8.09 8.09 -8.08 8.08 8.08 -8.05 -8.04 8.03 8.00 -8.00 7.99 -7.99 -7.97 7.95 7.93 -7.92 7.92 7.85 7.84 -7.83 7.81 7.77 7.70 -7.68 3JBH Observed( ) Ideal( ) o 113.04 133.91 113.00 124.48 116.13 100.64 116.14 112.95 100.69 124.40 135.24 112.85 124.39 133.34 100.78 100.79 116.24 112.78 112.77 112.77 116.26 112.77 112.76 100.86 100.87 112.72 124.30 116.30 112.69 100.91 100.92 112.66 112.64 100.96 132.37 112.58 124.22 100.54 112.55 124.19 112.46 110.42 o 106.30 112.10 106.30 120.30 120.30 107.30 120.30 106.30 107.30 120.30 117.20 106.30 120.30 112.10 107.30 107.30 120.30 106.30 106.30 106.30 120.30 106.30 106.30 107.30 107.30 106.30 120.30 120.30 106.30 107.30 107.30 106.30 106.30 107.30 111.00 106.30 120.30 111.50 106.30 120.30 106.30 122.70 Continued on next page... Page 17 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 1 1 1 2 3 1 1 1 1 1 1 2 1 1 1 1 1 1 3 1 1 1 3 1 1 3 1 1 2 1 1 1 1 1 1 1 1 1 1 H G B H B H J L A B G H H G I B B G G B A K H G H K H A F B B D B B A B A G A A A B 792 792 788 435 830 505 21 154 591 792 828 33 591 828 21 33 505 33 268 435 363 118 788 896 505 154 828 206 154 795 809 21 792 505 364 591 640 435 500 896 792 788 TRP TRP TRP TRP TRP TRP TRP TRP TRP TRP TRP TRP TRP TRP TRP TRP TRP TRP ALA TRP GLN ARG TRP ARG TRP TRP TRP THR TRP TRP ARG TRP TRP TRP ARG TRP ARG TRP ARG ARG TRP TRP Atoms CD1-CG-CD2 CD1-CG-CD2 CD1-CG-CD2 CD1-CG-CD2 CE2-CD2-CG CD1-CG-CD2 CD1-CG-CD2 CE2-CD2-CG CE2-CD2-CG CD1-CG-CD2 CD1-CG-CD2 CE2-CD2-CG CE2-CD2-CG CE2-CD2-CG CE2-CD2-CG CD1-CG-CD2 CD1-CG-CD2 CD1-CG-CD2 CA-C-N CD1-CG-CD2 N-CA-CB NE-CZ-NH2 CE2-CD2-CG NE-CZ-NH1 CE2-CD2-CG CE2-CD2-CG CE2-CD2-CG O-C-N CE2-CD2-CG CE2-CD2-CG NE-CZ-NH1 CE2-CD2-CG CE2-CD2-CG CE2-CD2-CG NE-CZ-NH2 CD1-CG-CD2 NE-CZ-NH1 CE2-CD2-CG NE-CZ-NH2 NE-CZ-NH1 CD1-CG-CD2 CE2-CD2-CG Z 7.68 7.67 7.66 7.66 -7.65 7.65 7.65 -7.64 -7.64 7.64 7.64 -7.63 -7.63 -7.62 -7.61 7.61 7.61 7.59 7.57 7.54 -7.53 7.49 -7.48 -7.48 -7.48 -7.47 -7.47 -7.47 -7.46 -7.45 -7.42 -7.42 -7.40 -7.40 -7.39 7.39 -7.37 -7.35 7.35 -7.33 7.31 -7.30 3JBH Observed( ) Ideal( ) o 112.44 112.44 112.43 112.43 101.18 112.42 112.42 101.18 101.19 112.41 112.41 101.20 101.20 101.20 101.21 112.38 112.38 112.38 133.85 112.33 97.05 124.04 101.31 116.56 101.32 101.32 101.33 110.75 101.33 101.34 116.59 101.37 101.38 101.38 116.60 112.21 116.62 101.42 123.97 116.64 112.15 101.46 o 106.30 106.30 106.30 106.30 107.30 106.30 106.30 107.30 107.30 106.30 106.30 107.30 107.30 107.30 107.30 106.30 106.30 106.30 117.20 106.30 110.60 120.30 107.30 120.30 107.30 107.30 107.30 122.70 107.30 107.30 120.30 107.30 107.30 107.30 120.30 106.30 120.30 107.30 120.30 120.30 106.30 107.30 Continued on next page... Page 18 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 2 1 1 1 1 1 2 1 1 1 1 1 3 1 1 1 3 1 1 3 1 1 1 1 1 2 2 1 1 2 1 3 1 1 1 1 1 1 1 3 1 1 I A B G A H J G B G A A E H G G L A H K A H A G G D D G G D A L A G B A G G B L H A 13 435 828 450 673 795 21 591 591 926 363 654 192 792 654 268 195 792 794 192 268 435 33 593 830 21 134 795 795 134 830 13 794 792 380 795 33 830 435 195 12 365 ARG TRP TRP ARG ARG TRP TRP TRP TRP ARG GLN ARG GLU TRP ARG ALA GLY TRP ARG GLU ALA TRP TRP GLU TRP TRP ASP TRP TRP ASP TRP SER ARG TRP ARG TRP TRP TRP TRP GLY TYR PRO Atoms NE-CZ-NH2 CE2-CD2-CG CE2-CD2-CG NE-CZ-NH1 NE-CZ-NH1 CE2-CD2-CG CE2-CD2-CG CE2-CD2-CG CE2-CD2-CG NE-CZ-NH2 CA-CB-CG NE-CZ-NH2 O-C-N CE2-CD2-CG NE-CZ-NH2 O-C-N O-C-N CE2-CD2-CG NE-CZ-NH1 O-C-N CA-C-N CE2-CD2-CG CE2-CD2-CG CA-CB-CG CD1-CG-CD2 CD1-CG-CD2 CA-C-N CD1-CG-CD2 CE2-CD2-CG O-C-N CD1-CG-CD2 CA-C-N NE-CZ-NH1 CE2-CD2-CG NE-CZ-NH2 CE2-CD2-CG CE2-CD2-CG CE2-CD2-CG CE2-CD2-CG CA-C-N CB-CG-CD2 CA-C-N Z 7.28 -7.27 -7.27 -7.26 -7.26 -7.25 -7.25 -7.23 -7.22 7.22 7.22 7.21 -7.21 -7.21 7.20 -7.19 -7.19 -7.15 -7.15 -7.14 7.13 -7.12 -7.12 7.12 7.11 7.11 7.09 7.08 -7.06 -7.05 7.04 7.01 -6.99 -6.99 6.96 -6.96 -6.93 -6.89 -6.88 6.86 -6.85 -6.84 3JBH Observed( ) Ideal( ) o 123.94 101.48 101.49 116.67 116.67 101.50 101.50 101.52 101.52 123.91 129.29 123.91 111.17 101.54 123.90 111.19 111.20 101.58 116.73 111.27 132.89 101.60 101.60 129.06 111.99 111.99 130.38 111.96 101.65 111.21 111.94 132.62 116.81 101.71 123.78 101.73 101.75 101.79 101.79 132.28 116.89 102.15 o 120.30 107.30 107.30 120.30 120.30 107.30 107.30 107.30 107.30 120.30 113.40 120.30 122.70 107.30 120.30 122.70 122.70 107.30 120.30 122.70 117.20 107.30 107.30 113.40 106.30 106.30 116.20 106.30 107.30 123.20 106.30 117.20 120.30 107.30 120.30 107.30 107.30 107.30 107.30 117.20 121.00 117.20 Continued on next page... Page 19 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 3 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 3 3 1 1 3 1 1 1 3 1 1 1 1 1 1 2 1 3 L A B B A G A A H G B J A A H B B A A A A A G A K F B B E A A G L H A G A G A J B F 42 830 64 872 828 640 364 312 364 450 640 37 767 788 439 33 439 781 364 795 673 603 809 313 195 14 708 708 192 268 451 422 31 280 788 712 306 157 240 30 364 88 ARG TRP ARG LYS TRP ARG ARG GLN ARG ARG ARG ARG ARG TRP ARG TRP ARG ARG ARG TRP ARG VAL ARG GLY GLY LYS ARG ARG GLU ALA GLN GLY PRO TYR TRP PRO ASP TYR ARG ARG ARG ARG Atoms NE-CZ-NH1 CE2-CD2-CG NE-CZ-NH1 CG-CD-CE CB-CG-CD1 NE-CZ-NH1 CD-NE-CZ N-CA-C NE-CZ-NH2 NE-CZ-NH2 NE-CZ-NH1 NE-CZ-NH1 NE-CZ-NH2 CG-CD2-CE3 NE-CZ-NH1 CB-CG-CD1 NE-CZ-NH2 NE-CZ-NH1 N-CA-C CD1-CG-CD2 NE-CZ-NH2 N-CA-C NE-CZ-NH2 O-C-N O-C-N N-CA-C NE-CZ-NH1 NE-CZ-NH2 CA-C-N O-C-N O-C-N CA-C-N N-CD-CG CB-CG-CD2 CB-CG-CD1 N-CA-C CA-C-N CB-CG-CD2 NE-CZ-NH2 NE-CZ-NH1 NE-CZ-NH2 NE-CZ-NH2 Z -6.84 -6.83 -6.79 6.78 -6.73 -6.71 -6.71 6.70 6.67 6.64 6.61 -6.61 6.61 6.60 -6.60 -6.56 6.56 -6.55 6.54 6.49 6.47 6.47 6.46 -6.43 -6.39 6.37 -6.32 6.30 6.30 -6.29 -6.29 6.26 -6.26 -6.25 -6.25 6.24 -6.23 -6.22 6.19 -6.18 6.18 6.17 3JBH Observed( ) Ideal( ) o 116.88 101.83 116.91 132.24 118.25 116.94 114.21 129.08 123.64 123.62 123.61 117.00 123.60 139.84 117.00 118.47 123.58 117.03 128.66 111.49 123.53 128.46 123.53 112.42 112.48 128.19 117.14 123.45 131.06 112.63 112.63 128.72 93.81 117.25 118.87 128.33 103.49 117.27 123.40 117.21 123.39 123.38 o 120.30 107.30 120.30 111.90 127.00 120.30 123.60 111.00 120.30 120.30 120.30 120.30 120.30 133.90 120.30 127.00 120.30 120.30 111.00 106.30 120.30 111.00 120.30 122.70 122.70 111.00 120.30 120.30 117.20 122.70 122.70 116.20 103.20 121.00 127.00 112.10 117.20 121.00 120.30 120.30 120.30 120.30 Continued on next page... Page 20 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 3 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 K A A B G B G D B G H A H A B H B G H L K B H G A H B A G A A A A G H B B B A A B G 192 363 368 500 788 500 705 127 659 788 796 596 380 831 641 33 905 313 871 31 149 642 773 828 828 164 941 712 596 373 498 64 103 498 412 33 103 452 778 313 926 603 GLU GLN GLU ARG TRP ARG ARG ARG ARG TRP TYR LYS ARG TYR LYS TRP ARG GLY ARG PRO ARG LYS ARG TRP TRP ARG ARG PRO LYS ASP TYR ARG ARG TYR ARG TRP ARG TYR ARG GLY ARG VAL Atoms CA-C-N N-CA-C N-CA-C NE-CZ-NH1 CG-CD2-CE3 NE-CZ-NH2 NE-CZ-NH1 NE-CZ-NH2 NE-CZ-NH1 CB-CG-CD1 CB-CG-CD1 CA-CB-CG NE-CZ-NH1 CB-CG-CD2 O-C-N CB-CG-CD1 NE-CZ-NH1 O-C-N NE-CZ-NH1 N-CA-CB NE-CZ-NH1 CA-C-N NE-CZ-NH2 CB-CG-CD1 CG-CD2-CE3 NE-CZ-NH1 NE-CZ-NH1 N-CA-C CA-CB-CG CB-CG-OD1 CB-CG-CD2 NE-CZ-NH1 NE-CZ-NH1 CB-CG-CD2 NE-CZ-NH1 CG-CD2-CE3 NE-CZ-NH1 CB-CG-CD2 NE-CZ-NH2 CA-C-N NE-CZ-NH2 N-CA-C Z 6.14 6.13 6.11 -6.11 6.09 6.08 -6.07 6.05 -6.02 -6.02 -6.02 6.01 -6.01 -6.00 -6.00 -5.99 -5.99 -5.99 -5.98 -5.97 -5.95 5.93 5.93 -5.92 5.92 5.91 -5.88 5.87 5.86 5.84 -5.83 -5.82 -5.82 -5.81 -5.81 5.81 -5.81 -5.80 5.80 5.79 5.77 5.75 3JBH Observed( ) Ideal( ) o 130.71 127.55 127.51 117.24 139.38 123.34 117.27 123.32 117.29 119.18 117.39 126.63 117.30 117.40 113.11 119.21 117.31 113.12 117.31 96.04 117.32 128.07 123.27 119.30 139.23 123.26 117.36 127.36 126.28 123.56 117.50 117.39 117.39 117.51 117.39 139.13 117.40 117.52 123.20 129.95 123.19 126.54 o 117.20 111.00 111.00 120.30 133.90 120.30 120.30 120.30 120.30 127.00 121.00 113.40 120.30 121.00 122.70 127.00 120.30 122.70 120.30 102.60 120.30 116.20 120.30 127.00 133.90 120.30 120.30 112.10 113.40 118.30 121.00 120.30 120.30 121.00 120.30 133.90 120.30 121.00 120.30 117.20 120.30 111.00 Continued on next page... Page 21 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 2 3 3 1 1 1 1 1 1 3 2 1 3 3 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 3 1 1 1 1 3 J K F H A A B G H L D A E F A A H H B E H G H H G H A G G B G H H B C C F H A G G E 116 42 13 673 568 795 269 640 673 67 57 505 118 195 431 773 673 767 210 195 565 505 830 598 820 33 871 33 142 12 887 830 724 872 21 21 195 141 375 505 788 154 ARG ARG SER ARG PRO TRP ARG ARG ARG ASP ARG TRP ARG GLY ARG ARG ARG ARG LYS GLY PRO TRP TRP PRO ARG TRP ARG TRP ARG TYR ASP TRP TYR LYS TRP TRP GLY ARG THR TRP TRP TRP Atoms NE-CZ-NH1 NE-CZ-NH1 O-C-N NE-CZ-NH1 CA-N-CD CB-CG-CD1 NE-CZ-NH2 NE-CZ-NH2 N-CA-CB N-CA-C NE-CZ-NH2 CG-CD2-CE3 NE-CZ-NH1 O-C-N NE-CZ-NH2 NE-CZ-NH2 NE-CZ-NH2 NE-CZ-NH1 O-C-N O-C-N CA-N-CD CG-CD2-CE3 CG-CD2-CE3 N-CA-C NE-CZ-NH1 CG-CD2-CE3 NE-CZ-NH1 CB-CG-CD1 NE-CZ-NH2 CB-CG-CD1 CB-CG-OD1 CB-CG-CD1 CB-CG-CD2 CB-CG-CD CG-CD1-NE1 CG-CD2-CE3 CA-C-N NE-CZ-NH2 CA-C-N CG-CD1-NE1 CG-CD1-NE1 CG-CD1-NE1 Z -5.75 -5.75 -5.73 -5.73 -5.72 -5.72 5.72 5.71 -5.71 5.71 5.70 5.68 -5.68 -5.68 5.67 5.67 5.67 -5.64 -5.63 -5.63 -5.63 5.61 5.58 5.57 -5.57 5.57 -5.56 -5.56 5.56 5.55 5.55 -5.55 -5.54 5.52 -5.52 5.51 5.51 5.49 5.48 -5.48 -5.47 -5.44 3JBH Observed( ) Ideal( ) o 117.43 117.43 113.53 117.44 103.49 119.56 123.16 123.16 100.32 126.40 123.15 139.02 117.46 113.61 123.13 123.13 123.14 117.48 113.69 113.69 103.62 138.95 138.92 126.59 117.51 138.91 117.52 119.77 123.08 124.33 123.30 119.78 117.68 125.96 104.58 138.85 129.32 123.04 129.25 104.62 104.63 104.66 o 120.30 120.30 122.70 120.30 111.50 127.00 120.30 120.30 110.60 111.00 120.30 133.90 120.30 122.70 120.30 120.30 120.30 120.30 122.70 122.70 111.50 133.90 133.90 112.10 120.30 133.90 120.30 127.00 120.30 121.00 118.30 127.00 121.00 111.60 110.10 133.90 117.20 120.30 117.20 110.10 110.10 110.10 Continued on next page... Page 22 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 3 2 1 1 3 2 1 1 1 2 1 2 1 3 1 1 1 3 1 1 1 1 1 1 1 3 1 3 3 1 1 1 1 1 1 1 3 1 1 1 G A L D G H E I B H B I G D G L A H B E H A A A G B H F G L L A A A G B G H L A H G 828 809 31 13 313 659 154 139 565 137 280 21 64 37 786 17 505 439 637 154 140 505 189 360 327 830 809 67 597 17 154 207 367 640 431 210 596 19 154 591 86 773 TRP ARG PRO ARG GLY ARG TRP TYR PRO TYR TYR TRP ARG ARG VAL SER TRP ARG GLY TRP ARG TRP TYR LYS ARG TRP ARG ASP ASP SER TRP LYS GLU ARG ARG LYS LYS ARG TRP TRP SER ARG Atoms CG-CD2-CE3 NE-CZ-NH2 O-C-N NE-CZ-NH1 CA-C-N NE-CZ-NH2 CG-CD2-CE3 CB-CG-CD2 CA-N-CD CB-CG-CD2 CB-CG-CD2 CB-CG-CD1 NE-CZ-NH2 NE-CZ-NH1 CA-CB-CG2 N-CA-C CG-CD1-NE1 NE-CZ-NH2 CA-C-N CB-CG-CD1 NE-CZ-NH1 CB-CG-CD1 CB-CG-CD1 O-C-N NE-CZ-NH1 CB-CG-CD1 NE-CZ-NH1 N-CA-C N-CA-C O-C-N CG-CD2-CE3 N-CA-CB C-N-CA NE-CZ-NH2 NE-CZ-NH2 CA-C-N N-CA-CB NE-CZ-NH1 CG-CD1-NE1 CG-CD1-NE1 N-CA-C NE-CZ-NH2 Z 5.44 5.43 -5.42 -5.42 5.41 5.41 5.40 -5.40 -5.39 -5.39 -5.38 -5.37 5.37 -5.37 5.36 5.34 -5.33 5.33 5.32 -5.32 -5.32 -5.30 -5.30 -5.30 -5.30 -5.29 -5.29 5.28 5.28 -5.28 5.27 5.27 5.27 5.26 5.25 5.25 -5.24 -5.24 -5.24 -5.24 5.22 5.21 3JBH Observed( ) Ideal( ) o 138.80 123.01 114.02 117.59 129.10 123.00 138.76 117.76 103.95 117.77 117.77 120.02 122.99 117.61 118.93 125.43 104.77 122.96 126.85 120.08 117.64 120.11 117.82 114.22 117.65 120.12 117.65 125.27 125.27 114.26 138.64 120.08 134.87 122.93 122.93 128.75 101.17 117.68 104.86 104.86 125.09 122.91 o 133.90 120.30 122.70 120.30 117.20 120.30 133.90 121.00 111.50 121.00 121.00 127.00 120.30 120.30 110.90 111.00 110.10 120.30 116.20 127.00 120.30 127.00 121.00 122.70 120.30 127.00 120.30 111.00 111.00 122.70 133.90 110.60 121.70 120.30 120.30 117.20 110.60 120.30 110.10 110.10 111.00 120.30 Continued on next page... Page 23 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 3 1 2 1 1 1 2 1 3 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 3 1 1 1 1 1 1 1 1 1 3 1 1 1 2 F B C H H G I H L I B A B A H H A B G G I A G A B A A F A B G H H H B G B F B B A J 16 637 21 637 771 820 156 453 39 21 828 450 164 795 28 234 788 146 422 659 21 365 246 142 132 33 596 154 364 870 591 619 828 505 149 137 141 118 830 505 140 139 LYS GLY TRP GLY LEU ARG LYS PHE ARG TRP TRP ARG ARG TRP GLY ARG TRP PRO GLY ARG TRP PRO ARG ARG ARG TRP LYS TRP ARG VAL TRP PHE TRP TRP LEU TYR ARG ARG TRP TRP ARG TYR Atoms O-C-N O-C-N CB-CG-CD1 CA-C-N CA-CB-CG NE-CZ-NH2 CB-CG-CD N-CA-C NE-CZ-NH2 CG-CD2-CE3 CG-CD1-NE1 NE-CZ-NH2 NE-CZ-NH2 CG-CD2-CE3 O-C-N NE-CZ-NH2 CG-CD1-NE1 N-CA-CB O-C-N NE-CZ-NH2 CG-CD1-NE1 CA-CB-CG NE-CZ-NH2 NE-CZ-NH1 NE-CZ-NH1 CB-CG-CD1 N-CA-CB CG-CD2-CE3 CA-C-N CA-C-N CG-CD1-NE1 N-CA-C CG-CD1-NE1 CG-CD2-CE3 N-CA-C CB-CG-CD2 NE-CZ-NH2 NE-CZ-NH1 CG-CD1-NE1 CG-CD2-CE3 NE-CZ-NH2 CB-CG-CD1 Z -5.20 -5.20 -5.20 5.20 5.20 5.19 -5.19 5.18 5.16 5.15 -5.14 5.14 5.14 5.13 -5.12 5.11 -5.10 -5.10 -5.10 5.09 -5.09 -5.09 5.08 -5.08 -5.08 -5.07 -5.07 5.06 5.06 5.05 -5.05 5.05 -5.05 5.05 5.04 -5.04 5.03 -5.03 -5.01 5.01 5.01 -5.00 3JBH Observed( ) Ideal( ) o 114.38 114.36 120.24 126.60 127.25 122.90 98.11 124.98 122.88 138.54 104.95 122.87 122.87 138.52 114.51 122.86 105.00 96.99 114.53 122.84 105.01 94.33 122.84 117.76 117.76 120.41 101.48 138.46 131.26 128.32 105.05 124.64 105.05 138.44 124.60 117.98 122.81 117.79 105.09 138.41 122.81 118.00 o 122.70 123.20 127.00 116.20 115.30 120.30 111.60 111.00 120.30 133.90 110.10 120.30 120.30 133.90 122.70 120.30 110.10 102.60 123.20 120.30 110.10 104.00 120.30 120.30 120.30 127.00 110.60 133.90 117.10 117.20 110.10 111.00 110.10 133.90 111.00 121.00 120.30 120.30 110.10 133.90 120.30 121.00 Continued on next page... Page 24 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 G 367 GLU Atoms C-N-CA Z 5.00 Observed( ) Ideal( ) o 134.21 There are no chirality outliers. All (116) planarity outliers are listed below: Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 A A A A A A A A A A A A A A A A A A A A A A A A A A A A B B B B B B B B 110 142 157 190 269 272 280 307 310 361 363 364 366 393 41 410 412 418 567 586 64 640 708 724 757 796 831 871 103 190 26 278 366 41 419 450 TYR ARG TYR TYR ARG SER TYR TYR VAL PHE GLN ARG ARG TYR TYR GLN ARG SER LYS TYR ARG ARG ARG TYR TYR TYR TYR ARG ARG TYR TYR ARG ARG TYR TYR ARG 3JBH Group Sidechain Sidechain Sidechain Sidechain Sidechain Peptide Sidechain Sidechain,Peptide Peptide Sidechain Sidechain,Mainchain,Peptide Sidechain Sidechain,Peptide Sidechain Sidechain Peptide Sidechain Peptide Peptide Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Continued on next page... o 121.70 Page 25 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 2 3 3 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 B B B B B B B B B B B B D E F F F G G G G G G G G G G G G G G G G G G G G G G G G H 526 621 627 639 645 654 659 673 708 714 867 941 111 80 113 80 9 10 123 157 164 190 272 273 305 307 347 366 41 410 418 452 586 64 640 654 724 757 817 831 926 110 GLY ASP ALA GLY SER ARG ARG ARG ARG ARG GLU ARG LEU ARG THR ARG LYS TYR TYR TYR ARG TYR SER GLN TYR TYR TYR ARG TYR GLN SER TYR TYR ARG ARG ARG TYR TYR ARG TYR ARG TYR Group Peptide Peptide Peptide Peptide Peptide Sidechain Sidechain Sidechain Sidechain Sidechain Peptide Sidechain Peptide Sidechain Peptide Sidechain Peptide Sidechain Sidechain Sidechain Sidechain Sidechain Peptide Peptide Sidechain,Peptide Sidechain Sidechain Peptide Sidechain Peptide Peptide Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Continued on next page... 3JBH Page 26 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 3 3 3 3 3 3 3 3 3 5.2 H H H H H H H H H H H H H H H H H H I J J J J K K L L L L L L L 112 140 142 164 26 278 347 419 462 571 621 627 647 654 673 767 79 941 93 111 116 13 136 38 80 113 29 30 31 32 39 80 Group TYR ARG ARG ARG TYR ARG TYR TYR PHE GLN ASP ALA GLN ARG ARG ARG TYR ARG TYR LEU ARG ARG PHE ARG ARG THR PRO PRO PRO LYS ARG ARG Too-close contacts 3JBH Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Peptide Peptide Peptide Peptide Sidechain Sidechain Sidechain Sidechain Sidechain Sidechain Peptide Sidechain Sidechain Peptide Sidechain Sidechain Peptide Peptide Mainchain Peptide Mainchain,Peptide Peptide Sidechain O i In the following table, the Non-H and H(model) columns list the number of non-hydrogen atoms and hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogen atoms added and optimized by MolProbity. The Clashes column lists the number of clashes within the asymmetric unit, whereas Symm-Clashes lists symmetry related clashes. Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 1 A 7721 0 7778 123 0 Continued on next page... Page 27 wwPDB EM Map/Model Validation Report 3JBH Continued from previous page... Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 1 1 1 2 2 2 2 3 3 3 3 All B G H C D I J E F K L All 7739 7721 7739 1233 1233 1233 1233 1529 1529 1529 1529 41968 0 0 0 0 0 0 0 0 0 0 0 0 7799 7778 7799 1227 1227 1227 1227 1491 1491 1491 1491 42026 165 108 130 9 9 10 14 27 28 23 47 606 0 0 0 0 0 0 0 0 0 0 0 0 The all-atom clashscore is dened as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 7. All (606) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. Atom-1 Atom-2 1:B:641:LYS:HE3 1:B:641:LYS:CE 1:A:364:ARG:HA 1:B:641:LYS:CE 1:A:364:ARG:HA 1:A:449:LYS:HD3 1:B:641:LYS:HE3 1:B:635:LYS:HE3 1:H:175:SER:HB2 1:B:641:LYS:HE3 1:A:369:GLN:HA 1:A:500:ARG:HG3 1:B:174:GLU:HB3 3:L:22:GLY:HA3 1:H:135:GLN:HG3 2:I:100:THR:HB 3:F:173:ASP:HB3 1:B:267:LYS:HD3 1:A:58:ILE:HB 1:A:833:LEU:HA 3:L:97:SER:HA 1:A:206:THR:HB 1:B:642:LYS:NZ 1:B:642:LYS:NZ 3:L:31:PRO:HG2 1:B:642:LYS:HZ1 3:L:31:PRO:CG 1:B:405:ASN:OD1 1:B:642:LYS:HZ2 1:B:904:GLU:HA 1:H:463:GLU:HA 1:B:642:LYS:HZ1 1:A:417:VAL:HG21 1:B:366:ARG:HB2 1:B:676:ILE:HD12 3:L:94:GLU:HG3 1:H:199:LYS:HE3 2:I:136:PHE:HB3 3:F:178:ILE:HG13 1:B:430:ASP:HB2 1:A:61:GLN:HB2 3:E:192:GLU:HG3 3:L:100:ALA:HB2 1:A:207:LYS:HB2 Interatomic distance (Å) 1.21 2.16 1.42 1.70 1.95 1.72 1.07 1.55 1.56 1.01 1.64 1.64 1.65 1.66 1.66 1.65 1.66 1.67 1.68 1.68 1.68 1.67 Clash overlap (Å) 1.52 1.08 1.00 0.99 0.94 0.90 0.90 0.87 0.87 0.80 0.80 0.79 0.79 0.78 0.77 0.77 0.77 0.77 0.76 0.76 0.76 0.76 Continued on next page... Page 28 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:B:641:LYS:HE3 3:E:51:PHE:HB3 1:G:58:ILE:HB 3:L:130:ASN:HA 3:E:192:GLU:HG2 1:B:642:LYS:HE2 3:L:173:ASP:HB3 1:A:879:VAL:HG12 1:H:561:VAL:HB 1:G:833:LEU:HA 2:I:101:MET:SD 1:B:902:VAL:HA 1:H:431:ARG:NH2 2:J:26:LYS:HD2 1:A:449:LYS:HA 1:A:271:ILE:HD12 1:G:716:VAL:HG12 1:H:597:ASP:HB3 1:B:7:PRO:HA 3:F:117:ASP:HA 1:B:13:ILE:HB 1:B:541:THR:HA 1:B:641:LYS:CE 1:A:37:GLU:HB2 1:G:779:ASP:HA 1:A:34:VAL:HG11 1:G:367:GLU:HB2 1:A:309:PHE:HB2 1:A:772:GLY:HA2 1:B:175:SER:HB2 1:A:364:ARG:HD2 3:K:51:PHE:HB2 1:H:244:PHE:O 1:A:539:LYS:HD2 1:B:716:VAL:HG13 1:A:366:ARG:HA 1:B:431:ARG:NH2 1:B:388:ASN:HB3 1:B:423:GLY:HA2 1:G:645:SER:HB3 1:A:100:LEU:HB3 1:B:642:LYS:CE 3:E:56:VAL:HG21 1:G:61:GLN:HB2 3:L:133:ASN:HB3 3:E:193:GLU:HA 1:B:903:GLU:OE1 3:L:178:ILE:HG13 1:B:450:ARG:HB2 1:H:576:SER:HB2 3:K:192:GLU:HG3 2:I:139:TYR:HB3 1:B:905:ARG:HB2 1:H:619:PHE:HA 2:J:61:LYS:HD3 1:A:449:LYS:HE2 1:A:419:TYR:HA 1:G:763:LYS:HE2 1:H:646:PHE:HD2 1:B:12:TYR:HE2 3:F:120:ALA:HB3 1:B:108:LEU:HD22 1:B:592:LEU:HD11 1:B:642:LYS:HZ2 1:A:38:LYS:HD3 1:G:782:LEU:HB2 1:A:58:ILE:HD12 1:G:369:GLN:H 3:L:18:GLU:HG3 1:A:775:GLU:HG3 1:B:463:GLU:HA 1:A:371:GLU:H 3:L:61:GLU:HG2 1:H:260:ILE:HA 2:J:3:ASP:HB2 1:B:718:PRO:HD2 3:L:39:ARG:HB2 1:B:619:PHE:HA 1:B:391:ASP:HB2 1:B:426:LYS:HE2 1:G:647:GLN:HG3 1:A:120:ILE:HD11 Interatomic distance (Å) 2.17 1.67 1.69 1.69 1.70 1.87 1.68 1.69 1.71 1.73 2.31 1.73 2.07 1.73 1.73 1.75 1.75 1.58 1.58 1.76 1.77 1.77 1.95 1.77 1.77 1.75 1.61 1.77 1.78 1.76 1.62 1.79 1.97 1.78 1.79 1.78 2.13 1.80 1.79 1.80 1.78 Clash overlap (Å) 0.75 0.75 0.74 0.74 0.74 0.73 0.73 0.73 0.72 0.70 0.70 0.70 0.70 0.69 0.69 0.69 0.69 0.68 0.68 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.66 0.66 0.65 0.65 0.65 0.65 0.65 0.64 0.64 0.64 0.64 0.64 0.64 0.64 0.63 Continued on next page... 3JBH Page 29 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:B:743:THR:HA 1:B:746:VAL:HG22 1:B:635:LYS:HB3 1:B:642:LYS:CD 1:B:97:LEU:HD11 1:B:692:MET:HA 1:A:712:PRO:HD2 1:A:767:ARG:HA 1:G:500:ARG:HG3 1:H:366:ARG:HB2 1:A:364:ARG:HA 3:L:31:PRO:HG3 2:D:34:ASP:HA 2:D:37:ARG:HD2 1:G:34:VAL:HG11 1:G:58:ILE:HD12 1:A:762:THR:HG21 1:B:371:GLU:HB3 1:H:131:ASN:O 1:H:135:GLN:HB2 1:H:356:LEU:HD22 1:H:425:ALA:HB2 1:B:635:LYS:HB3 1:B:642:LYS:HD3 1:B:833:LEU:HD23 3:F:192:GLU:HG2 1:B:904:GLU:O 1:B:908:LYS:HB2 1:H:231:LYS:HB3 1:H:278:ARG:H 1:H:231:LYS:HG3 1:H:236:ASP:HA 1:A:399:PRO:O 1:A:409:THR:HA 1:G:166:ASN:ND2 1:G:667:THR:HG22 1:H:13:ILE:HB 1:H:108:LEU:HD22 1:H:171:ILE:HG12 1:H:672:VAL:HB 1:G:884:GLU:HA 1:G:887:ASP:HB2 1:G:309:PHE:HB2 1:G:362:LYS:HE3 1:H:211:ALA:HB3 1:H:214:GLU:HG2 3:E:109:THR:HG23 3:F:70:LYS:HD3 1:G:46:ILE:HG23 1:G:54:CYS:SG 1:B:431:ARG:HH22 1:B:619:PHE:HA 3:L:69:ASP:HB2 3:L:73:PHE:HB2 1:B:481:LYS:HD3 1:B:520:LEU:HA 1:G:785:ILE:HG23 1:G:786:VAL:HG23 1:G:37:GLU:HB2 1:G:38:LYS:HD3 1:H:84:ASP:HA 1:H:112:TYR:HB2 1:B:84:ASP:HA 1:B:112:TYR:HB2 1:B:142:ARG:HG2 1:B:145:VAL:HB 1:B:640:ARG:NH1 1:B:896:ARG:HG3 1:G:791:ALA:HB2 2:I:44:THR:HG22 1:H:498:TYR:HB3 1:H:503:ILE:HG12 1:H:743:THR:HA 1:H:746:VAL:HG22 1:A:256:ALA:HB1 1:A:447:LYS:HG3 1:G:287:MET:SD 1:G:360:LYS:HE2 1:H:141:ARG:NH1 1:H:776:GLU:HA 1:B:493:LEU:HA 1:B:496:GLU:HB2 Interatomic distance (Å) 1.81 2.28 1.81 1.81 1.81 1.80 1.81 1.82 1.81 2.00 1.82 1.80 1.82 2.01 1.66 1.83 2.01 2.16 1.83 1.82 1.82 1.84 1.82 1.84 2.41 1.66 1.83 1.84 1.83 1.82 1.84 1.84 1.85 2.17 1.85 1.83 1.83 1.84 2.43 2.18 1.86 Clash overlap (Å) 0.63 0.62 0.62 0.62 0.62 0.62 0.62 0.62 0.62 0.62 0.62 0.61 0.61 0.61 0.61 0.61 0.61 0.61 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.58 0.58 0.58 0.58 Continued on next page... 3JBH Page 30 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:H:114:GLY:HA2 1:H:712:PRO:HG3 1:A:109:ILE:HG21 1:A:122:PRO:HD3 1:A:884:GLU:HA 1:A:887:ASP:HB2 2:I:131:GLU:HG2 2:I:137:LEU:HD11 1:G:118:VAL:HG12 1:G:673:ARG:HB3 1:G:243:LYS:HB3 1:G:458:ASP:HB3 1:G:713:ASN:HB2 1:G:766:PHE:HB2 1:H:635:LYS:HB2 1:H:643:GLY:H 1:A:923:LEU:HD23 1:A:926:ARG:HH11 1:B:210:LYS:HB3 1:B:211:ALA:HA 3:K:20:GLU:HG3 3:K:109:THR:HG21 1:A:785:ILE:HG23 1:A:786:VAL:HG23 1:B:141:ARG:NH1 1:B:776:GLU:HA 1:H:546:GLN:HE22 1:H:575:PHE:HB3 3:K:109:THR:HG23 3:L:70:LYS:HD3 1:B:157:TYR:HB2 1:B:190:TYR:HE2 1:H:250:GLY:HA2 1:H:450:ARG:HB3 1:A:308:HIS:HA 3:L:13:SER:HB3 1:B:832:LYS:HD3 3:F:191:ALA:HB3 1:B:836:LYS:HB3 3:E:46:ASN:HB3 1:H:632:GLY:H 1:H:644:ALA:HB2 1:B:356:LEU:HD21 1:B:421:VAL:O 1:H:356:LEU:HD21 1:H:421:VAL:O 1:H:423:GLY:HA2 1:H:426:LYS:HE2 1:H:267:LYS:HD3 1:H:430:ASP:HB2 3:K:192:GLU:HG2 3:K:193:GLU:HA 1:B:168:SER:OG 1:B:669:PRO:HA 1:H:726:ILE:HG12 1:H:785:ILE:HB 1:B:231:LYS:HG3 1:B:236:ASP:HA 3:E:30:PRO:HB3 3:E:37:LYS:HD3 1:B:864:LEU:O 1:B:868:GLU:HG2 1:H:541:THR:HA 1:H:592:LEU:HD11 3:K:41:GLN:HG2 3:L:194:GLU:HG3 3:F:132:PHE:HB3 3:F:142:CYS:SG 1:H:457:LEU:HD23 1:H:482:LEU:HD13 1:A:906:LEU:HD13 1:B:906:LEU:HA 1:H:295:LYS:HA 1:H:300:LEU:HD12 1:H:480:GLU:HG2 1:H:518:ILE:HG12 1:B:871:ARG:HB3 1:B:872:LYS:HD3 1:G:743:THR:HA 1:G:746:VAL:HG12 1:B:642:LYS:CE 1:B:903:GLU:OE1 Interatomic distance (Å) 1.85 1.86 1.86 1.85 1.85 1.84 1.85 1.69 1.69 1.86 1.86 1.86 2.19 1.69 1.86 1.68 1.86 1.86 1.86 1.86 1.68 2.05 2.05 1.87 1.88 1.87 2.06 1.86 1.87 1.87 2.06 1.88 1.88 2.45 1.88 1.87 1.87 1.87 1.89 1.88 2.55 Clash overlap (Å) 0.58 0.58 0.58 0.58 0.58 0.58 0.58 0.58 0.58 0.58 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.57 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.55 0.55 0.55 0.55 0.55 0.55 0.55 0.55 Continued on next page... 3JBH Page 31 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:A:832:LYS:O 1:H:138:LYS:HA 1:B:91:LEU:HD23 1:G:712:PRO:HD2 1:B:219:GLN:HB3 2:D:140:GLU:HB3 1:B:83:GLU:HG3 1:H:542:ASP:HB3 1:A:570:GLN:HE21 1:A:874:ILE:HD12 1:B:740:LYS:O 1:B:868:GLU:HG3 1:A:118:VAL:HA 1:A:593:GLU:HG2 1:H:231:LYS:HB3 1:G:134:VAL:HG13 1:B:635:LYS:CE 1:H:732:VAL:HG11 1:A:33:TRP:HB2 1:A:711:PHE:HB3 1:G:451:GLN:HB3 1:B:146:PRO:HB2 1:B:811:ALA:HA 1:A:134:VAL:HG13 1:B:673:ARG:HH21 1:G:100:LEU:HB3 1:H:832:LYS:HD3 3:E:74:ILE:HG23 3:K:74:ILE:HG23 1:A:599:VAL:HG11 1:B:732:VAL:HG11 1:G:256:ALA:HB1 1:G:951:LEU:HD11 1:H:747:LEU:HB3 2:I:94:ASP:HB2 3:L:58:GLU:HA 1:G:599:VAL:HG22 1:H:15:MET:SD 1:H:157:TYR:HB2 3:K:51:PHE:HB3 1:G:245:ILE:HG23 3:E:192:GLU:HA 1:H:193:VAL:HG13 1:B:705:ARG:HG2 1:G:767:ARG:HA 1:B:332:ALA:HB1 2:D:141:PRO:HD3 1:B:84:ASP:H 1:H:588:ILE:HG22 2:J:26:LYS:HG3 1:B:871:ARG:HD2 1:B:743:THR:HG22 1:B:869:LYS:HD2 1:A:673:ARG:O 1:A:598:PRO:HB3 1:H:278:ARG:HB2 1:G:189:TYR:HE1 1:B:904:GLU:HA 1:H:742:VAL:HG23 1:A:72:GLN:HB2 1:A:765:PHE:HB3 1:G:452:TYR:HA 1:B:147:PRO:HD2 3:F:127:VAL:HG13 1:A:189:TYR:HE1 1:B:673:ARG:HB3 1:G:120:ILE:HD11 3:L:191:ALA:HB3 3:E:78:ASP:HB2 3:K:78:ASP:HB2 1:A:604:VAL:HG23 1:B:742:VAL:HG23 1:G:447:LYS:HG3 1:H:952:LYS:HE3 1:H:752:LEU:HD23 2:I:139:TYR:HE2 3:L:61:GLU:HB2 1:G:603:VAL:HG23 1:H:82:CYS:HA 1:H:190:TYR:HE2 3:K:56:VAL:HG21 1:G:260:ILE:HG12 Interatomic distance (Å) 2.06 1.89 1.89 1.89 1.89 1.87 1.72 1.89 1.71 1.90 2.07 1.90 2.07 1.89 1.89 1.73 2.34 1.89 1.90 1.89 1.90 1.91 1.91 1.73 1.72 1.90 1.90 1.91 1.91 1.91 1.89 1.91 1.90 1.90 1.73 1.91 1.91 2.50 1.74 1.91 1.90 Clash overlap (Å) 0.55 0.55 0.55 0.55 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.53 0.52 0.52 0.52 0.52 0.52 0.52 Continued on next page... 3JBH Page 32 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:G:354:MET:SD 1:A:721:LYS:NZ 1:H:330:ASP:CG 1:A:837:VAL:HG21 1:B:154:ASP:HA 1:H:265:LEU:HD23 1:G:422:GLY:HA2 3:L:132:PHE:HB3 1:G:84:ASP:HB3 1:H:356:LEU:HD11 1:H:54:CYS:SG 1:H:677:PRO:HB2 2:J:27:ILE:HG13 1:B:175:SER:HB3 1:B:169:MET:HB3 1:H:167:GLN:NE2 1:H:166:ASN:HB3 1:B:271:ILE:HA 1:H:119:ALA:O 1:H:146:PRO:HB2 1:H:145:VAL:HG12 1:H:724:TYR:HE2 1:B:5:PRO:HG3 2:D:41:CYS:O 1:B:138:LYS:HA 1:B:930:GLU:HA 1:H:283:PHE:HB3 1:H:144:GLU:O 1:H:237:ASN:OD1 3:F:69:ASP:HB2 1:H:493:LEU:HA 1:A:309:PHE:CE2 1:A:55:THR:HA 1:B:726:ILE:HG12 2:C:48:VAL:HG12 1:A:830:TRP:HA 1:H:521:ILE:HB 2:J:140:GLU:HB3 3:L:6:LYS:HD3 1:G:435:TRP:O 1:H:240:ARG:HB3 1:G:358:GLU:HG3 1:B:379:GLU:OE1 1:H:343:LYS:HZ1 3:E:86:LEU:HA 1:B:189:TYR:CZ 1:H:430:ASP:HA 1:G:425:ALA:H 3:L:142:CYS:SG 1:G:87:ASN:HD22 1:H:424:LEU:HB3 1:H:56:VAL:HG23 1:H:686:ILE:HA 2:J:62:LEU:HB2 1:B:234:ARG:NH2 1:B:456:VAL:HG22 1:H:668:GLN:HB3 1:H:667:THR:HG22 1:B:309:PHE:CE1 1:H:674:CYS:HA 1:H:147:PRO:HD2 1:H:151:ALA:HB2 1:H:747:LEU:HD23 1:B:769:GLY:HA2 2:D:43:PRO:HD3 1:B:193:VAL:HG13 1:B:933:ALA:HB3 1:H:354:MET:SD 1:H:146:PRO:HD3 1:H:281:HIS:HE1 3:F:73:PHE:HB2 1:H:496:GLU:HB2 3:L:31:PRO:N 1:A:65:GLN:HA 1:B:785:ILE:HB 2:C:53:GLY:HA3 3:E:195:GLY:HA3 1:H:524:PRO:HD2 2:J:141:PRO:HD3 3:L:9:LYS:O 1:G:439:ARG:HG2 1:H:266:GLU:HB2 Interatomic distance (Å) 2.49 2.34 2.12 1.91 2.45 1.91 1.75 2.49 1.74 1.91 2.49 1.92 1.91 2.24 1.92 2.25 1.93 2.46 2.10 1.92 1.93 1.74 1.92 2.10 1.93 1.91 2.51 2.11 1.94 1.94 1.93 2.80 1.93 1.93 1.93 1.94 1.94 1.93 2.11 2.12 1.92 Clash overlap (Å) 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 Continued on next page... 3JBH Page 33 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:B:278:ARG:HD2 1:A:170:LEU:HD13 1:G:883:GLN:OE1 3:L:59:PHE:O 1:A:892:LEU:HD22 1:H:169:MET:O 3:L:92:GLU:HA 1:G:795:TRP:HZ3 1:A:875:GLU:O 1:B:497:GLU:HG2 1:B:636:GLY:H 1:G:310:VAL:HB 1:A:690:LEU:O 1:B:635:LYS:HE3 3:F:22:GLY:HA3 1:H:167:GLN:HE22 2:J:68:LEU:HB2 1:H:721:LYS:HB3 2:I:103:ALA:HB2 3:E:51:PHE:HB2 3:F:188:THR:HG22 1:G:84:ASP:HB3 1:A:451:GLN:HB3 1:A:716:VAL:HG21 1:H:97:LEU:HD12 3:E:67:ASP:O 1:G:285:GLN:NE2 1:H:484:GLN:HA 3:K:67:ASP:O 1:A:435:TRP:O 1:B:248:HIS:HA 1:H:930:GLU:HA 1:H:109:ILE:HG23 1:H:210:LYS:HB3 1:H:714:ARG:HA 1:A:372:ALA:HB3 1:G:221:ASN:HB3 1:G:863:SER:O 1:A:134:VAL:HG11 1:A:461:GLY:HA2 1:G:588:ILE:O 1:B:315:ILE:O 1:A:482:LEU:HD11 1:H:450:ARG:HG3 3:L:63:PHE:HB2 1:A:896:ARG:HH22 1:H:456:VAL:HA 3:L:95:LEU:HG 2:I:40:ASP:HA 1:A:879:VAL:HG23 1:B:668:GLN:HG3 1:B:643:GLY:HA3 1:G:311:SER:HA 1:A:694:GLN:HG3 1:B:904:GLU:CA 3:F:94:GLU:HG2 1:H:668:GLN:HB3 2:J:69:PRO:HD3 2:J:92:VAL:HG12 2:I:137:LEU:HD13 3:F:61:GLU:HG2 3:F:189:LYS:H 1:G:87:ASN:ND2 1:A:452:TYR:HA 1:B:390:ALA:HA 1:H:695:LEU:HD12 3:E:70:LYS:NZ 1:G:326:LEU:HB2 1:H:484:GLN:OE1 3:K:70:LYS:NZ 1:A:439:ARG:HG2 1:B:452:TYR:O 1:H:933:ALA:HB3 1:H:120:ILE:O 1:H:211:ALA:HA 1:H:764:VAL:O 1:A:377:GLU:HA 1:G:222:PRO:HD3 1:G:867:GLU:HG2 1:A:192:ASN:OD1 1:A:479:ASN:OD1 1:G:591:TRP:HB2 Interatomic distance (Å) 2.12 1.94 2.12 2.11 1.76 2.11 1.93 1.77 2.13 1.94 1.78 1.94 2.12 2.34 1.94 1.78 1.95 1.95 1.95 1.95 1.78 2.27 1.95 1.93 1.94 2.47 2.27 2.13 2.46 2.14 2.14 1.95 2.14 1.95 2.13 1.96 1.96 2.14 2.14 2.14 2.14 Clash overlap (Å) 0.50 0.50 0.50 0.50 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.49 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 0.48 Continued on next page... 3JBH Page 34 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:H:171:ILE:HA 1:G:109:ILE:HG21 1:B:419:TYR:OH 3:E:20:GLU:HG3 1:B:244:PHE:O 3:F:33:PRO:HA 1:G:119:ALA:O 1:A:232:THR:O 1:A:789:LEU:O 1:B:356:LEU:HD22 2:J:136:PHE:O 1:A:119:ALA:O 1:B:530:ILE:HG12 1:G:56:VAL:HG22 1:H:169:MET:HB3 1:H:563:PRO:HB2 1:B:141:ARG:HH12 1:H:817:ARG:NH2 1:A:55:THR:HG22 1:B:711:PHE:HA 3:F:126:ASP:O 1:B:157:TYR:HA 1:H:894:SER:HA 3:K:52:THR:HB 1:A:662:ALA:O 1:B:526:GLY:CA 1:A:420:SER:O 1:A:353:CYS:SG 1:A:867:GLU:OE1 1:H:278:ARG:HD2 1:A:272:SER:HB2 1:G:107:ASN:O 1:H:141:ARG:HH12 1:B:242:GLY:O 1:H:33:TRP:HB2 2:J:60:LYS:HZ1 1:B:142:ARG:HH11 1:A:362:LYS:H 1:A:6:ASP:OD1 1:B:640:ARG:HH12 3:F:141:LYS:NZ 1:H:672:VAL:O 1:G:122:PRO:HD3 1:B:426:LYS:NZ 3:E:109:THR:HG21 1:B:260:ILE:HA 3:F:34:PRO:HD3 1:G:674:CYS:HA 1:A:236:ASP:HA 1:A:793:ILE:HG13 1:B:425:ALA:HB2 2:J:138:LYS:NZ 1:A:674:CYS:HA 1:B:548:LYS:HB2 1:G:64:ARG:O 1:H:456:VAL:HG22 1:H:566:PRO:HD2 1:B:779:ASP:CG 3:L:123:ASP:OD2 1:A:65:GLN:HB3 1:B:712:PRO:HD3 3:F:130:ASN:HB2 1:B:160:MET:HG2 1:H:897:SER:OG 3:K:55:GLN:HE21 1:A:665:HIS:HB2 1:B:654:ARG:HD3 1:A:423:GLY:HA3 1:A:428:MET:SD 1:B:872:LYS:HD2 1:H:315:ILE:O 1:A:418:SER:HB2 1:G:109:ILE:HG23 1:H:779:ASP:CG 1:B:262:THR:HA 1:H:72:GLN:HB2 2:J:66:GLU:CD 1:B:151:ALA:HB1 3:L:32:LYS:HE3 1:A:7:PRO:HD3 1:B:896:ARG:HG3 3:F:173:ASP:O Interatomic distance (Å) 2.13 1.95 2.47 1.95 2.14 1.83 2.13 2.14 2.15 1.95 2.43 2.14 1.95 2.13 1.96 1.95 2.18 2.48 1.96 1.72 2.15 1.97 2.15 1.80 2.15 2.45 2.14 3.13 2.15 2.15 1.97 2.15 2.18 2.15 1.96 2.18 1.80 1.80 2.14 1.79 2.46 Clash overlap (Å) 0.48 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 Continued on next page... 3JBH Page 35 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 3:F:79:ILE:HG21 1:G:80:GLU:HG3 1:H:215:ASP:O 3:L:79:ILE:HG13 1:A:571:GLN:HG2 1:B:256:ALA:O 1:B:7:PRO:HA 1:A:836:LYS:HB2 3:E:192:GLU:CG 1:G:571:GLN:HG2 1:H:192:ASN:HA 1:H:845:LYS:HE2 2:J:83:LEU:HD21 1:A:575:PHE:HD2 3:F:30:PRO:HA 1:A:713:ASN:HB2 1:H:142:ARG:HD3 1:A:309:PHE:HD2 1:B:168:SER:O 3:F:54:HIS:HB2 1:H:402:LYS:HE2 1:H:248:HIS:HA 2:I:90:LEU:HD22 1:B:546:GLN:HE22 1:G:378:GLY:HA2 3:K:33:PRO:HA 1:G:164:ARG:O 1:H:358:GLU:HB2 1:A:137:TYR:O 1:A:629:GLU:HB2 1:B:104:TYR:HE2 1:B:231:LYS:HB3 1:H:103:ARG:HG2 3:K:107:ASN:OD1 1:B:168:SER:HA 1:B:845:LYS:HE2 3:E:153:THR:O 1:G:273:GLN:HG2 1:G:691:VAL:O 1:H:131:ASN:ND2 1:H:17:GLN:NE2 3:F:99:VAL:HG22 1:G:102:GLN:HE22 1:H:219:GLN:HG2 3:L:99:VAL:HG13 1:A:572:GLU:HB2 1:B:446:THR:HA 1:B:12:TYR:CE2 3:E:192:GLU:HB3 3:E:193:GLU:HA 1:G:572:GLU:HB2 1:H:197:THR:HG21 1:H:848:ASP:HB3 2:J:147:ILE:HG21 1:A:588:ILE:HD11 3:F:31:PRO:HD2 1:A:766:PHE:HB2 1:H:713:ASN:OD1 3:L:18:GLU:HG3 1:B:670:HIS:HB2 3:F:57:GLN:OE1 1:H:405:ASN:HA 1:H:452:TYR:O 2:I:139:TYR:HB2 1:B:575:PHE:HB3 1:G:381:VAL:HG23 3:K:34:PRO:HD3 1:H:400:LYS:HE3 1:H:377:GLU:HB3 1:A:140:ARG:HG2 1:A:640:ARG:HA 1:B:686:ILE:HB 1:B:278:ARG:HB2 1:H:111:THR:OG1 3:K:109:THR:HB 1:B:455:GLY:O 1:B:848:ASP:HB3 3:E:157:LYS:NZ 1:G:277:GLU:HB2 1:G:695:LEU:HG 1:H:207:LYS:HD3 1:H:81:LYS:HB2 Interatomic distance (Å) 1.97 1.79 2.14 1.96 1.95 2.15 2.44 1.98 2.43 1.97 1.98 1.97 1.96 1.80 1.84 1.97 2.14 1.80 2.15 2.16 1.97 2.16 1.98 1.80 1.97 1.83 2.16 1.97 2.15 1.98 1.80 1.98 2.15 2.16 2.16 1.98 2.44 1.99 2.16 2.31 2.31 Clash overlap (Å) 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.46 0.45 0.45 0.45 0.45 0.45 0.45 0.45 Continued on next page... 3JBH Page 36 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 3:L:193:GLU:HB2 1:G:174:GLU:HB2 1:B:142:ARG:NH1 1:B:423:GLY:O 1:B:701:LEU:HG 1:B:953:LYS:NZ 1:G:115:LEU:HD23 3:L:90:CYS:SG 1:B:567:LYS:HB3 1:B:504:ASP:HB3 1:G:93:ASP:HB3 1:H:132:ARG:HB2 2:C:90:LEU:HD22 1:G:264:LEU:HD22 1:A:364:ARG:C 1:A:46:ILE:HG23 1:G:355:HIS:HB3 3:K:192:GLU:CG 1:A:309:PHE:HE2 1:B:141:ARG:NH2 1:G:891:GLN:HA 3:K:57:GLN:HB3 1:A:565:PRO:HA 1:G:137:TYR:HE2 1:B:868:GLU:HA 2:C:37:ARG:HA 1:H:953:LYS:NZ 1:A:375:THR:HA 1:B:817:ARG:NH2 1:A:947:GLU:HB3 1:G:420:SER:O 1:G:91:LEU:HD13 1:H:119:ALA:HB3 1:H:167:GLN:O 1:B:142:ARG:HD3 1:B:522:GLU:OE2 1:H:647:GLN:OE1 1:H:702:GLU:HG3 1:A:561:VAL:HB 1:A:367:GLU:HB3 1:G:367:GLU:HB3 3:L:194:GLU:H 1:G:676:ILE:HD11 1:B:151:ALA:HB1 1:B:426:LYS:HG2 1:B:705:ARG:HH21 1:B:957:ASP:OD2 1:G:490:MET:SD 3:L:95:LEU:HD23 1:B:568:PRO:HD3 1:B:758:ARG:HD2 1:G:701:LEU:HD22 1:H:204:ALA:HB1 2:C:139:TYR:HB2 1:G:474:CYS:HB2 3:L:31:PRO:HG2 1:A:54:CYS:SG 1:G:381:VAL:HG22 3:K:193:GLU:HA 3:L:31:PRO:HD2 2:D:112:SER:O 1:G:891:GLN:HE21 3:L:60:LYS:NZ 1:A:566:PRO:HD2 1:G:151:ALA:HB2 1:B:872:LYS:HG2 2:C:41:CYS:O 1:H:957:ASP:OD2 1:A:377:GLU:HG3 3:F:123:ASP:OD2 1:B:948:ILE:HD11 1:G:423:GLY:HA3 1:G:705:ARG:HG2 1:H:674:CYS:SG 1:H:454:ILE:HA 1:B:713:ASN:OD1 1:B:658:ASN:HB2 1:H:648:THR:HA 1:H:705:ARG:NH1 1:A:576:SER:HB2 1:A:368:GLU:HB2 1:G:368:GLU:HB2 Interatomic distance (Å) 1.70 1.98 2.32 2.16 1.81 2.49 2.56 2.57 1.99 1.99 1.98 1.98 1.98 1.98 2.37 2.57 1.99 2.46 1.82 2.50 1.82 2.32 1.86 1.82 1.99 2.17 2.50 1.99 2.50 2.00 2.18 1.98 2.57 2.17 2.17 2.18 2.17 2.33 1.99 1.99 1.98 Clash overlap (Å) 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 Continued on next page... 3JBH Page 37 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:G:422:GLY:O 1:G:832:LYS:O 1:G:901:ASP:HB3 1:A:795:TRP:HA 1:B:790:GLN:O 3:F:11:LYS:HB2 1:G:837:VAL:HG21 1:B:495:GLN:HA 1:B:926:ARG:HG2 3:F:66:ILE:HG23 1:H:246:ARG:O 1:H:601:ASP:HB3 1:A:468:ASN:HB2 1:B:521:ILE:HB 2:C:138:LYS:O 1:G:222:PRO:HA 1:G:682:GLN:HA 1:G:815:ILE:HD11 1:A:716:VAL:HG12 1:A:757:TYR:HB3 1:B:563:PRO:HB2 1:B:868:GLU:CA 1:G:232:THR:OG1 1:A:134:VAL:HG13 1:B:714:ARG:HA 1:B:836:LYS:O 1:A:832:LYS:HB3 1:G:561:VAL:HB 1:H:141:ARG:HH11 3:L:11:LYS:HB2 1:B:488:HIS:O 1:H:159:ALA:HB2 1:H:400:LYS:HA 1:G:830:TRP:HA 1:A:268:ALA:N 1:B:246:ARG:HA 1:B:723:ARG:HD2 1:G:717:TYR:CE1 1:H:668:GLN:OE1 1:A:782:LEU:HA 1:B:871:ARG:HB3 1:G:426:LYS:HB2 3:K:192:GLU:HA 1:H:523:LYS:HD3 2:C:37:ARG:HD3 1:B:794:ARG:HG2 3:F:11:LYS:HE3 3:K:86:LEU:HA 1:B:498:TYR:CD1 1:B:929:ARG:HD2 3:F:82:THR:HG21 1:H:258:ALA:HA 1:H:629:GLU:HG2 1:A:585:PRO:O 1:B:524:PRO:HD2 2:C:141:PRO:HD2 1:G:225:GLU:HB2 1:G:683:PRO:HD2 3:K:183:PHE:HE1 1:A:763:LYS:HE2 1:A:770:VAL:HG11 1:B:566:PRO:HD2 1:B:872:LYS:HG2 1:G:238:SER:HB3 1:A:189:TYR:CE1 1:B:764:VAL:O 1:B:836:LYS:HD2 3:E:191:ALA:O 1:G:576:SER:HB2 1:H:776:GLU:HA 3:L:11:LYS:HE3 1:B:492:VAL:HB 1:H:714:ARG:O 1:H:400:LYS:HD3 3:K:195:GLY:HA3 1:A:269:ARG:HB2 1:B:454:ILE:O 2:D:112:SER:HB2 1:G:764:VAL:HB 1:H:763:LYS:NZ 1:A:785:ILE:HG13 1:B:872:LYS:HE2 Interatomic distance (Å) 2.18 2.17 2.00 1.99 2.18 1.81 1.99 2.53 1.98 1.99 2.18 2.00 2.18 1.99 2.17 2.00 1.90 1.81 2.00 2.00 2.00 2.48 2.17 2.51 2.18 2.18 2.18 2.00 1.83 1.75 2.18 2.18 1.84 1.98 2.34 2.17 2.00 2.53 2.51 2.01 2.00 Clash overlap (Å) 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.44 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 Continued on next page... 3JBH Page 38 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:H:298:LEU:HA 1:H:384:LEU:HD21 2:J:93:TYR:CZ 2:J:101:MET:HA 1:A:364:ARG:O 3:L:31:PRO:HG2 1:A:231:LYS:HA 1:A:236:ASP:O 1:A:835:ILE:O 1:A:839:PRO:HD2 1:G:164:ARG:HH11 1:H:606:GLN:NE2 1:A:166:ASN:ND2 1:A:667:THR:HG22 1:A:85:MET:HA 1:A:88:LEU:HD13 1:B:869:LYS:O 1:B:873:ASP:HB2 1:G:629:GLU:HB2 1:G:640:ARG:HA 1:G:55:THR:HA 1:G:65:GLN:HA 1:H:331:THR:HA 1:H:334:ASP:OD2 1:H:5:PRO:HG3 1:H:769:GLY:HA2 2:J:22:GLU:HB3 3:L:154:TRP:HZ2 1:A:926:ARG:O 1:A:929:ARG:HB3 1:B:523:LYS:O 1:B:527:ILE:HG13 1:A:792:TRP:CZ3 2:C:147:ILE:HA 1:H:701:LEU:O 1:H:705:ARG:HG3 1:A:107:ASN:O 1:A:109:ILE:HG23 1:A:17:GLN:OE1 1:A:20:LYS:NZ 1:B:233:VAL:HG22 1:B:275:THR:O 3:E:90:CYS:HB3 3:E:94:GLU:HB2 1:G:17:GLN:OE1 1:G:20:LYS:NZ 1:G:661:MET:O 1:G:665:HIS:HD2 1:G:843:MET:SD 3:K:57:GLN:HB2 1:H:126:PHE:HB3 1:H:128:ILE:HG13 3:L:33:PRO:HB2 3:L:34:PRO:CD 1:A:599:VAL:HG22 1:A:603:VAL:HG23 1:B:155:GLY:HA2 1:B:158:SER:OG 1:B:701:LEU:HG 1:B:705:ARG:NH2 1:B:31:MET:HB2 1:B:74:VAL:HG11 1:G:710:GLY:O 1:G:767:ARG:NH2 1:A:557:SER:HA 1:A:558:PRO:HD3 1:A:690:LEU:HG 1:A:694:GLN:HE21 1:B:119:ALA:O 1:B:674:CYS:HA 3:E:28:PRO:HA 3:E:29:PRO:HD3 1:G:575:PHE:HD2 1:G:588:ILE:HD11 1:A:367:GLU:HB2 1:A:369:GLN:H 1:A:923:LEU:HD21 1:B:924:GLN:HG2 1:G:377:GLU:HB3 1:G:393:TYR:OH 1:H:159:ALA:HA 1:H:715:MET:HA Interatomic distance (Å) 1.99 2.54 2.18 2.18 2.17 2.17 2.34 2.01 2.19 2.00 2.01 2.18 2.00 1.84 2.18 2.18 2.54 2.19 2.19 2.51 2.19 2.01 2.52 2.01 2.59 2.00 2.48 2.01 2.18 2.33 2.01 2.51 1.87 1.84 2.19 1.86 1.83 1.84 2.01 2.19 2.01 Clash overlap (Å) 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 0.43 Continued on next page... 3JBH Page 39 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:A:310:VAL:HG12 1:A:311:SER:HA 1:B:240:ARG:HB2 1:B:280:TYR:HE2 1:B:534:GLU:OE1 1:B:537:PHE:CD1 1:B:531:LEU:HG 1:B:595:ASN:ND2 1:B:109:ILE:HG21 1:B:122:PRO:HD3 1:B:875:GLU:O 1:B:878:ASN:HB3 3:E:33:PRO:HA 3:E:34:PRO:HD3 3:E:57:GLN:HB3 3:F:60:LYS:NZ 3:L:14:LYS:HD3 3:L:103:PRO:HB2 1:B:54:CYS:O 1:B:65:GLN:HA 1:B:668:GLN:OE1 1:B:763:LYS:NZ 1:H:371:GLU:HG2 1:H:397:VAL:HG21 1:B:480:GLU:HG2 1:B:518:ILE:HG12 1:B:75:ASN:HA 1:B:76:PRO:HD3 1:G:232:THR:O 1:G:236:ASP:HA 1:G:195:ALA:HB1 1:G:197:THR:HG23 1:H:342:TYR:HA 1:H:345:ASP:HB2 1:H:503:ILE:HG22 1:H:760:GLY:HA2 3:L:102:ALA:HB1 3:L:106:ILE:HD11 3:L:23:ASP:HA 3:L:93:GLN:NE2 1:B:654:ARG:HE 1:B:654:ARG:HA 1:B:721:LYS:HB3 2:D:92:VAL:HG12 3:E:72:GLY:O 3:E:107:ASN:HA 1:G:497:GLU:O 1:G:501:GLU:HG2 1:A:282:ILE:HA 1:A:285:GLN:OE1 1:B:702:GLU:HG3 1:B:705:ARG:NH1 1:B:743:THR:HG23 1:B:744:GLU:OE2 1:A:80:GLU:HG3 1:A:102:GLN:HE22 1:G:468:ASN:HB2 1:G:585:PRO:O 3:L:188:THR:HG22 3:L:189:LYS:H 1:B:501:GLU:O 1:B:761:ASN:HB2 3:F:13:SER:HA 3:F:15:LYS:N 1:H:1:MET:HA 1:H:4:ASP:O 1:G:923:LEU:HD13 1:H:923:LEU:HB3 1:B:716:VAL:HG22 1:B:762:THR:HG22 2:D:83:LEU:HD21 2:D:147:ILE:HG21 1:H:512:LEU:HB3 1:H:580:TYR:OH 1:H:711:PHE:HA 1:H:712:PRO:HD3 1:G:906:LEU:HD13 1:H:906:LEU:HA 1:A:782:LEU:HD13 2:C:92:VAL:HB 1:B:157:TYR:CZ 1:B:161:LEU:HD11 Interatomic distance (Å) 2.01 1.83 2.72 2.34 1.99 2.20 1.86 2.34 2.00 2.20 2.51 2.01 2.02 1.89 2.19 2.02 2.01 2.01 2.00 2.34 1.84 2.02 2.20 2.19 2.19 2.34 2.20 1.85 2.20 1.83 2.20 2.35 2.20 2.02 2.02 2.01 2.20 1.73 2.01 2.01 2.54 Clash overlap (Å) 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.41 0.41 Continued on next page... 3JBH Page 40 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:G:134:VAL:HG13 1:H:142:ARG:HG2 1:A:132:ARG:HG3 1:A:500:ARG:HD2 2:D:22:GLU:CD 3:E:51:PHE:HA 3:E:83:PHE:HB3 1:G:282:ILE:HA 1:G:97:LEU:HD11 1:H:528:LEU:HD12 1:H:804:LYS:HE3 1:B:727:LEU:HG 1:G:667:THR:O 1:H:654:ARG:HE 3:K:104:GLY:HA3 3:K:16:LYS:NZ 1:A:364:ARG:CB 1:B:717:TYR:HE1 3:E:5:GLU:OE2 1:G:889:PHE:HA 1:A:181:GLU:OE2 1:B:402:LYS:NZ 2:D:19:TYR:O 3:E:43:SER:HA 1:H:541:THR:HG23 1:A:406:GLU:HB3 1:A:501:GLU:O 1:G:131:ASN:ND2 1:G:217:VAL:HA 1:G:271:ILE:HD12 1:G:718:PRO:HG2 1:H:530:ILE:HG12 3:L:30:PRO:HA 1:A:715:MET:O 1:A:779:ASP:HA 1:B:829:LEU:O 1:G:715:MET:O 1:G:769:GLY:O 1:G:843:MET:HG2 1:A:309:PHE:CD2 1:A:883:GLN:NE2 1:G:189:TYR:CE1 1:H:145:VAL:HB 1:A:205:PRO:HB2 1:B:367:GLU:HB3 2:D:61:LYS:HZ3 3:E:56:VAL:HG11 3:E:89:LEU:HG 1:G:285:GLN:OE1 1:G:688:SER:HB3 1:H:529:SER:HB3 3:L:134:LEU:O 1:B:782:LEU:HD21 1:G:669:PRO:HD3 1:H:654:ARG:HA 3:K:105:PRO:HD3 3:K:17:SER:OG 1:A:369:GLN:O 1:B:743:THR:HG21 3:F:90:CYS:HB3 1:G:892:LEU:HD12 1:A:185:LYS:NZ 1:B:630:LYS:O 2:D:21:TRP:HD1 3:F:193:GLU:O 1:H:544:SER:H 2:J:5:LYS:HG2 1:B:364:ARG:NH2 1:G:204:ALA:O 1:G:220:THR:OG1 1:G:419:TYR:HA 1:H:389:ALA:HB1 1:H:548:LYS:HB2 3:L:31:PRO:HD3 1:A:763:LYS:HD2 1:A:782:LEU:HB2 3:F:195:GLY:HA3 1:G:763:LYS:HD2 1:G:773:ARG:N 3:L:53:GLN:O 3:L:18:GLU:HG3 1:B:451:GLN:HB3 Interatomic distance (Å) 2.54 2.01 2.01 2.01 2.22 2.01 2.01 2.20 2.02 2.01 2.21 2.01 2.20 1.85 1.84 2.46 2.68 1.85 2.20 2.02 2.53 2.46 2.02 2.20 1.84 2.03 2.54 2.54 2.20 2.02 2.02 2.02 1.84 2.20 2.02 2.21 2.20 2.54 2.20 2.55 2.35 Clash overlap (Å) 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 Continued on next page... 3JBH Page 41 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:B:309:PHE:HD1 1:B:309:PHE:HA 1:B:400:LYS:HD3 1:B:400:LYS:HA 2:C:94:ASP:HB2 2:C:139:TYR:HE2 1:G:372:ALA:HB3 1:G:377:GLU:HG2 1:G:33:TRP:HE1 1:G:74:VAL:HA 1:G:815:ILE:HD13 1:G:815:ILE:HA 1:H:110:TYR:OH 1:H:185:LYS:NZ 1:H:300:LEU:HA 1:H:307:TYR:OH 1:H:523:LYS:HB3 1:H:523:LYS:HE2 1:H:234:ARG:NH2 1:H:676:ILE:HD13 1:A:11:LEU:HD11 1:A:148:HIS:HB2 1:A:710:GLY:O 1:A:767:ARG:NH2 1:B:230:ALA:HB1 1:B:278:ARG:O 1:B:491:PHE:O 1:B:495:GLN:HG2 1:G:286:LEU:HD11 1:G:298:LEU:HD22 1:G:483:GLN:O 1:G:486:PHE:HB3 1:G:919:GLN:HA 1:G:922:GLU:HG2 1:A:364:ARG:HG3 3:L:36:GLN:HG3 3:K:5:GLU:OE2 3:L:90:CYS:HB3 1:A:369:GLN:HG2 1:A:417:VAL:HG11 1:B:9:GLU:CD 1:B:132:ARG:HH11 1:B:260:ILE:H 1:B:441:ASN:ND2 1:B:612:ASN:O 1:B:614:LEU:N 3:L:141:LYS:NZ 3:L:173:ASP:O 1:B:283:PHE:HB3 1:B:354:MET:SD 3:E:33:PRO:HB2 3:E:36:GLN:NE2 1:G:892:LEU:HD22 1:G:896:ARG:HH22 1:A:364:ARG:HH11 3:L:33:PRO:HD3 1:B:163:ASN:HD21 1:B:165:GLU:HB3 1:B:169:MET:O 1:B:456:VAL:HA 3:F:9:LYS:O 3:F:13:SER:HB3 1:H:175:SER:HB3 1:H:234:ARG:NH2 1:H:635:LYS:HB2 1:H:643:GLY:N 1:H:723:ARG:HD2 2:J:112:SER:HB2 2:I:143:VAL:O 2:I:146:ILE:HB 2:C:91:LYS:HD3 2:C:97:GLU:HG2 1:G:527:ILE:HG23 1:G:549:LEU:HD11 1:G:793:ILE:HG23 2:I:125:ILE:HD12 3:K:41:GLN:HA 3:L:85:SER:O 1:A:41:TYR:HD1 1:A:97:LEU:HD22 1:A:922:GLU:HG3 1:A:923:LEU:N Interatomic distance (Å) 1.79 1.91 1.86 2.03 1.86 1.95 2.51 2.20 1.89 2.35 2.02 2.54 2.21 2.20 2.02 2.20 2.01 2.03 2.21 2.03 2.25 2.19 2.54 2.47 2.60 2.36 1.86 1.85 1.87 2.21 2.21 2.36 2.36 2.03 2.22 2.03 2.04 2.02 2.21 1.87 2.36 Clash overlap (Å) 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 Continued on next page... 3JBH Page 42 wwPDB EM Map/Model Validation Report Continued from previous page... Atom-1 Atom-2 1:B:309:PHE:CD1 1:B:330:ASP:CG 1:B:248:HIS:ND1 1:B:715:MET:O 3:F:68:GLN:OE1 1:H:162:ALA:O 1:B:41:TYR:HD1 1:B:831:TYR:HD2 1:G:599:VAL:HG11 1:H:7:PRO:HA 1:B:357:GLY:HA3 1:B:343:LYS:HZ1 1:B:453:PHE:HB3 1:B:763:LYS:HA 3:F:78:ASP:HB2 1:H:164:ARG:NH2 1:B:97:LEU:HD22 3:F:194:GLU:HB3 1:G:604:VAL:HG23 1:H:12:TYR:CE2 Interatomic distance (Å) 2.57 2.24 2.37 2.21 2.21 2.55 1.86 1.86 2.04 2.56 3JBH Clash overlap (Å) 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 There are no symmetry-related clashes. 5.3 Torsion angles O i 5.3.1 Protein backbone O i In the following table, the Percentiles column shows the percent Ramachandran outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all EM entries. The Analysed column shows the number of residues for which the backbone conformation was analysed, and the total number of residues. Mol Chain Analysed 1 A 960/1953 (49%) 1 B 1 Favoured Allowed Outliers Percentiles 772 (80%) 149 (16%) 39 (4%) 3 35 962/1953 (49%) 779 (81%) 128 (13%) 55 (6%) 2 28 G 960/1953 (49%) 783 (82%) 136 (14%) 41 (4%) 3 34 1 H 962/1953 (49%) 779 (81%) 125 (13%) 58 (6%) 2 26 2 C 154/156 (99%) 137 (89%) 13 (8%) 4 (3%) 7 45 2 D 154/156 (99%) 139 (90%) 11 (7%) 4 (3%) 7 45 2 I 154/156 (99%) 135 (88%) 16 (10%) 3 (2%) 10 52 2 J 154/156 (99%) 131 (85%) 19 (12%) 4 (3%) 7 45 3 E 194/196 (99%) 139 (72%) 40 (21%) 15 (8%) 1 20 3 F 194/196 (99%) 136 (70%) 41 (21%) 17 (9%) 1 17 3 K 194/196 (99%) 144 (74%) 37 (19%) 13 (7%) 1 24 3 L 194/196 (99%) 129 (66%) 46 (24%) 19 (10%) 1 14 Continued on next page... Page 43 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain All All Analysed Favoured Allowed Outliers Percentiles 5236/9220 (57%) 4203 (80%) 761 (14%) 272 (5%) All (272) Ramachandran outliers are listed below: Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 3 3 3 3 3 3 3 3 A A A A A A A A A A A A A B B B B B B B B B B B B B B B D E E E F F F F F 6 22 138 269 310 311 363 365 393 394 568 603 845 68 86 142 149 178 205 367 565 613 621 646 680 725 733 869 152 17 47 50 14 15 53 105 125 ASP GLN LYS ARG VAL SER GLN PRO TYR LYS PRO VAL LYS LYS SER ARG LEU GLY PRO GLU PRO LYS ASP PHE LEU THR PRO LYS PRO SER VAL MET LYS LYS GLN PRO GLU Continued on next page... 3JBH 5 30 Page 44 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 3 3 3 3 3 3 3 3 3 3 1 1 1 1 1 F G G G G G G G G G G H H H H H H H H H H H H H H H I K L L L L L L L L L A A A A A 144 22 138 177 264 282 358 568 601 603 843 21 68 86 142 205 307 367 565 622 645 680 725 733 752 842 97 17 13 16 31 32 53 58 67 125 144 271 366 460 621 737 GLU GLN LYS ALA LEU ILE GLU PRO ASP VAL MET ASP LYS SER ARG PRO TYR GLU PRO HIS SER LEU THR PRO LEU THR GLU SER SER LYS PRO LYS GLN GLU ASP GLU GLU ILE ARG ALA ASP VAL Continued on next page... 3JBH Page 45 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 3 3 3 3 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 A A B B B B B B B B B B B B B B C C E E E F F F G G G G G G G G G H H H H H H H H H 831 843 14 274 312 446 447 451 517 535 645 752 834 842 844 870 97 152 55 59 139 63 174 195 269 271 308 516 621 712 735 737 831 3 11 178 356 580 613 621 646 648 TYR MET SER GLN GLN THR LYS GLN CYS SER SER LEU TYR THR ALA VAL GLU PRO GLN PHE GLU PHE GLY GLY ARG ILE HIS ALA ASP PRO GLY VAL TYR GLU LEU GLY LEU TYR LYS ASP PHE THR Continued on next page... 3JBH Page 46 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 3 3 3 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 3 3 3 3 1 1 1 1 1 1 1 1 1 1 H H H K K K L L A A A A A A A A A A B B B B B B B B C C E E E F G G G G G G H H H H 738 804 834 55 59 169 174 195 11 177 228 270 299 367 392 597 712 784 3 77 292 448 529 567 630 751 96 116 53 58 169 72 11 108 114 144 207 310 14 57 109 446 ASP LYS TYR GLN PHE GLU GLY GLY LEU ALA GLY VAL LEU GLU LEU ASP PRO LYS GLU PRO GLU GLN SER LYS LYS GLN ALA ARG GLN GLU GLU GLY LEU LEU GLY GLU LYS VAL SER ASP ILE THR Continued on next page... 3JBH Page 47 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 1 1 2 3 3 3 1 1 1 1 1 1 1 3 3 3 3 3 1 1 1 1 1 1 1 1 1 1 1 2 2 3 3 3 3 1 1 2 3 H H H H H J K L L A A B B B B B E F F F F G G G G G H H H H H H I J L L L L A B D E 529 567 573 751 844 152 139 72 192 207 827 20 57 601 804 871 106 28 57 95 192 9 392 460 784 827 137 200 251 375 639 803 116 130 70 80 188 190 735 618 40 21 SER LYS ALA GLN ALA PRO GLU GLY GLU LYS ASN LYS ASP ASP LYS ARG ILE PRO GLN LEU GLU GLU LEU ALA LYS ASN TYR PRO PRO THR GLY LYS ARG ASP LYS ARG THR GLY GLY ILE ASP GLY Continued on next page... 3JBH Page 48 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 3 3 1 1 1 1 1 1 1 1 1 1 2 2 3 3 1 1 1 1 1 1 2 3 1 1 1 2 3 3 3 1 1 1 2 3 3 1 1 3 1 1 E F G G G G H H H H H H J J K L A B B B B B D F G H H I K K L A A B D E E H H K G G 67 88 299 301 375 411 5 90 175 491 597 707 75 131 138 14 719 200 251 375 629 734 43 190 597 618 833 152 21 38 102 66 282 846 135 29 138 58 492 106 228 839 ASP ARG LEU SER THR GLY PRO TYR SER PHE ASP CYS LYS GLU GLY LYS ASP PRO PRO THR GLU LYS PRO GLY ASP ILE LEU PRO GLY ARG ALA VAL ILE VAL GLY PRO GLY ILE VAL ILE GLY PRO Continued on next page... 3JBH Page 49 wwPDB EM Map/Model Validation Report 3JBH Continued from previous page... Mol Chain Res Type 1 1 3 1 1 1 1 3 3 3 1 1 1 1 1 1 3 1 1 1 1 1 3 1 1 H H K B G G H K K K A A A B B B F G H H B B E G H 198 599 140 404 492 760 511 29 87 190 364 760 839 58 634 639 21 66 564 631 198 750 140 786 750 PRO VAL GLY GLY VAL GLY GLY PRO GLY GLY ARG GLY PRO ILE GLY GLY GLY VAL LYS GLY PRO ILE GLY VAL ILE 5.3.2 Protein sidechains O i In the following table, the Percentiles column shows the percent sidechain outliers of the chain as a percentile score with respect to all PDB entries followed by that with respect to all EM entries. The Analysed column shows the number of residues for which the sidechain conformation was analysed, and the total number of residues. Mol Chain Analysed 1 A 833/1689 (49%) 1 B 1 Rotameric Outliers Percentiles 792 (95%) 41 (5%) 31 67 835/1689 (49%) 780 (93%) 55 (7%) 21 57 G 833/1689 (49%) 798 (96%) 35 (4%) 36 70 1 H 835/1689 (49%) 785 (94%) 50 (6%) 24 60 2 C 132/132 (100%) 126 (96%) 6 (4%) 34 69 Continued on next page... Page 50 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Analysed 2 D 132/132 (100%) 2 I 2 Rotameric Outliers Percentiles 126 (96%) 6 (4%) 34 69 132/132 (100%) 127 (96%) 5 (4%) 40 73 J 132/132 (100%) 125 (95%) 7 (5%) 28 64 3 E 164/164 (100%) 157 (96%) 7 (4%) 35 70 3 F 164/164 (100%) 150 (92%) 14 (8%) 13 48 3 K 164/164 (100%) 160 (98%) 4 (2%) 57 82 3 L 164/164 (100%) 154 (94%) 10 (6%) 23 60 All All 4520/7940 (57%) 4280 (95%) 240 (5%) 33 64 All (240) residues with a non-rotameric sidechain are listed below: Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 A A A A A A A A A A A A A A A A A A A A A A A A A A A A 21 63 145 172 175 222 266 271 281 308 309 312 334 345 362 363 365 388 397 418 470 543 547 568 572 586 591 600 ASP SER VAL THR SER PRO GLU ILE HIS HIS PHE GLN ASP ASP LYS GLN PRO ASN VAL SER PHE LYS ASP PRO GLU TYR TRP ASN Continued on next page... 3JBH Page 51 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 A A A A A A A A A A A A A B B B B B B B B B B B B B B B B B B B B B B B B B B B B B 616 693 696 761 795 815 854 868 871 872 875 887 932 4 12 87 91 93 103 129 134 141 146 163 172 174 180 192 198 203 222 302 309 341 393 405 413 415 417 448 524 565 GLN HIS THR ASN TRP ILE GLU GLU ARG LYS GLU ASP ASP ASP TYR ASN LEU ASP ARG TYR VAL ARG PRO ASN THR GLU THR ASN PRO GLU PRO ASP PHE GLU TYR ASN ASN THR VAL GLN PRO PRO Continued on next page... 3JBH Page 52 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 B B B B B B B B B B B B B B B B B B B B B B B B B B C C C C C C D D D D D D E E E E 593 608 622 647 648 654 668 681 708 716 718 758 771 776 826 827 836 838 843 862 867 872 873 887 896 954 51 69 94 133 139 140 85 94 119 130 134 139 18 52 54 58 GLU LYS HIS GLN THR ARG GLN LYS ARG VAL PRO ARG LEU GLU ARG ASN LYS LYS MET GLU GLU LYS ASP ASP ARG GLU ASN PRO ASP ASP TYR GLU ASP ASP ASP ASP ASP TYR GLU THR HIS GLU Continued on next page... 3JBH Page 53 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 E E E F F F F F F F F F F F F F F G G G G G G G G G G G G G G G G G G G G G G G G G 59 71 108 3 17 19 30 42 52 55 64 67 89 105 113 118 168 4 21 26 165 212 215 222 266 271 306 334 345 362 391 470 538 543 547 568 586 591 600 605 616 668 PHE ASP PHE ASP SER GLU PRO ARG THR GLN GLN ASP LEU PRO THR ARG SER ASP ASP TYR GLU THR ASP PRO GLU ILE ASP ASP ASP LYS ASP PHE PRO LYS ASP PRO TYR TRP ASN ASP GLN GLN Continued on next page... 3JBH Page 54 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 G G G G G G G G G G H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H 702 713 721 756 761 795 854 865 883 904 4 12 83 91 92 93 103 134 141 145 146 180 192 203 222 236 302 341 405 473 522 524 565 571 593 597 601 608 641 642 645 649 GLU ASN LYS ASP ASN TRP GLU GLU GLN GLU ASP TYR GLU LEU ASN ASP ARG VAL ARG VAL PRO THR ASN GLU PRO ASP ASP GLU ASN LEU GLU PRO PRO GLN GLU ASP ASP LYS LYS LYS SER VAL Continued on next page... 3JBH Page 55 wwPDB EM Map/Model Validation Report Continued from previous page... Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 H H H H H H H H H H H H H H H H H H I I I I I J J J J J J J K K K K L L L L L L L L 668 681 716 743 771 794 826 836 838 843 862 868 887 896 923 925 948 954 42 51 94 119 140 63 85 94 119 130 139 153 54 58 59 108 3 45 55 67 68 89 97 113 GLN LYS VAL THR LEU ARG ARG LYS LYS MET GLU GLU ASP ARG LEU GLU ILE GLU LYS ASN ASP ASP GLU THR ASP ASP ASP ASP TYR ASP HIS GLU PHE PHE ASP SER GLN ASP GLN LEU SER THR Continued on next page... 3JBH Page 56 wwPDB EM Map/Model Validation Report 3JBH Continued from previous page... Mol Chain Res Type 3 3 L L 128 193 ILE GLU Some sidechains can be ipped to improve hydrogen bonding and reduce clashes. All (31) such sidechains are listed below: Mol Chain Res Type 1 1 1 1 1 1 1 1 1 1 2 2 2 3 3 1 1 1 1 1 1 1 1 1 1 1 1 2 2 3 3 A A A A A B B B B B C C D E F G G G G G H H H H H H H I I K L 148 281 570 668 921 148 163 441 595 693 51 73 108 54 130 87 281 665 670 891 75 107 192 281 546 616 670 51 73 55 55 HIS HIS GLN GLN GLN HIS ASN ASN ASN HIS ASN GLN HIS HIS ASN ASN HIS HIS HIS GLN ASN ASN ASN HIS GLN GLN HIS ASN GLN GLN GLN 5.3.3 RNA O i There are no RNA molecules in this entry. Page 57 5.4 wwPDB EM Map/Model Validation Report Non-standard residues in protein, DNA, RNA chains There are no non-standard protein/DNA/RNA residues in this entry. 5.5 Carbohydrates O i There are no carbohydrates in this entry. 5.6 Ligand geometry O i There are no ligands in this entry. 5.7 Other polymers O i There are no such residues in this entry. 5.8 Polymer linkage issues O There are no chain breaks in this entry. i 3JBH O i
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MolProbity Ramachandran analysis
97.8% (2392/2447) of all residues were in favored (98%) regions.
100.0% (2447/2447) of all residues were in allowed (>99.8%) regions.
There were no outliers.
wwPDB EM Map/Model Validation Report i
The table below summarises the geometric issues observed across the polymeric chains. The red,
orange, yellow and green segments on the bar indicate the fraction of residues that contain outliers
f...
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