Full wwpdb/emdatabank EM Map/Model Validation Report i

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1 Full wwpdb/emdatabank EM Map/Model Validation Report i Jan 9, :23 AM EST PDB ID : 6IRH EMDB ID: : EMD-9717 Title : Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/gl ycine-bound state at ph 6.3, Class III Authors : Zhang, J.; Chang, S.; Zhang, X.; Zhu, S. Deposited on : Resolution : 7.80 Å(reported) Based on PDB ID : 4PE5, 5TQ0, 5H8F This is a Full wwpdb/emdatabank EM Map/Model Validation Report for a publicly released PDB/EMDB entry. We welcome your comments at validation@mail.wwpdb.org A user guide is available at with specific help available everywhere you see the i symbol. MolProbity : 4.02b-467 Percentile statistics : v01 (using entries in the PDB archive December 27th 2017) Ideal geometry (proteins) : Engh & Huber (2001) Ideal geometry (DNA, RNA) : Parkinson et. al. (1996) Validation Pipeline (wwpdb-vp) : rb

2 Page 2 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1 Overall quality at a glance i The following experimental techniques were used to determine the structure: ELECTRON MICROSCOPY The reported resolution of this entry is 7.80 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 Whole archive EM structures (#Entries) (#Entries) Clashscore Ramachandran outliers Sidechain outliers 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 Quality of chain 1 A C B D 841

3 Page 3 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2 Entry composition i There are 2 unique types of molecules in this entry. The entry contains 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 Glutamate receptor ionotropic, NMDA 1. Mol Chain Residues Atoms AltConf Trace 1 C 786 Total C N O S A 785 Total C N O S There are 2 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference C 612 ARG GLY engineered mutation UNP Q05586 A 612 ARG GLY engineered mutation UNP Q05586 Molecule 2 is a protein called Glutamate receptor ionotropic, NMDA 2A. Mol Chain Residues Atoms AltConf Trace 2 D 756 Total C N O S B 756 Total C N O S There are 4 discrepancies between the modelled and reference sequences: Chain Residue Modelled Actual Comment Reference D 656 ARG GLU engineered mutation UNP Q12879 D 657 ARG GLU engineered mutation UNP Q12879 B 656 ARG GLU engineered mutation UNP Q12879 B 657 ARG GLU engineered mutation UNP Q12879

4 Page 4 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 3 Residue-property plots i These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic for a chain summarises the proportions of the various outlier classes displayed in the second graphic. The second graphic shows the sequence view annotated by issues in geometry. Residues are colorcoded 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: Glutamate receptor ionotropic, NMDA 1 Chain C: ARG LYS GLN F754 R755 S756 G757 F758 G761 M762 R763 N771 V772 S773 L774 S775 I776 L777 K778 S779 H780 E781 N782 G783 F784 D787 W792 V793 Q796 S802 ASN THR THR F810 E811 N812 M813 A814 G815 V816 F817 V820 I824 I828 I831 R839 R844 K678 F679 A682 T683 V684 K685 Q686 Y692 F693 R694 R695 Q696 V697 Y703 R704 H705 M706 E707 K708 H709 N710 Y711 A715 I718 Q719 A720 D723 N724 K725 L726 H727 A728 F729 I730 W731 A734 V735 L736 E737 F738 E739 A740 S741 Q742 L746 V747 T748 E751 L752 F753 S584 PHE GLY ARG PHE LYS VAL ASN SER GLU GLU GLU GLU GLU ASP L601 S605 A606 M607 W608 F609 S610 L614 L615 G620 E621 G622 ARG S626 F627 I631 L632 G633 W636 T648 L651 L657 D658 ARG GLU GLU R663 N668 R673 K496 E497 W498 N499 G500 M501 M502 G503 E504 L505 L506 S507 G508 Q509 A510 D511 M512 I513 I519 N520 N521 E522 R523 A524 Q525 Y526 I527 E528 F529 S530 K531 K534 Y535 Q536 G537 L538 T539 I540 L541 V542 K543 K544 P547 R548 SER THR ASP S553 F558 Q559 S560 W563 V573 G428 V431 K432 K433 V434 I435 C436 T437 G438 P439 N440 D441 T442 S446 P447 R448 H449 P452 Q453 C454 C455 Y456 G457 F458 D461 L462 L463 I464 K465 L466 A467 M470 N471 F472 T473 Y474 H477 L478 V479 A480 D481 G482 K483 F484 G485 T486 Q487 E488 R489 V490 N491 N494 K495 K347 N350 Y351 S352 I353 M354 N355 L356 R359 K360 L361 V362 Q363 V364 G365 I366 Y367 N368 H371 V372 I373 P374 N375 D376 R377 K378 I379 I380 W381 G384 G391 T396 R397 L398 K399 I400 V401 T402 I403 H404 Q405 E406 P407 F408 V409 Y410 V411 K412 P413 T414 E423 F424 Y245 V246 W247 L248 V249 G250 E251 R252 E253 I254 G265 I266 L267 I272 E277 H280 D283 V287 H293 T302 C308 V309 G310 N311 T312 N313 I314 W315 K316 T317 G318 P319 L320 F321 K322 R323 Y330 G333 V334 T335 V338 E339 F340 N341 G344 D345 R346 S159 W160 N161 H162 I163 I164 L165 L166 V167 S168 D169 D170 H171 E172 G173 Q177 K178 R179 L184 A191 E192 K193 V194 L195 Q196 F197 V204 T205 A206 L207 L208 M209 E210 L214 E215 A216 R217 V218 I219 I220 L221 T230 R233 A234 M237 L238 N239 M240 T241 G242 S243 G244 M74 A75 L76 S77 V78 C79 E80 D81 S85 S93 H94 P95 P96 T97 P98 T105 S108 Y109 T110 Y114 R115 L119 G120 L121 T122 T123 R124 M125 S126 I127 Y128 S129 H134 L138 R139 T140 V141 P142 P143 Y144 S145 H146 Q147 S148 S149 V150 W151 F152 E153 M154 M155 MET SER THR MET ARG THR PHE SER CYS SER VAL ARG CYS ASP K25 I26 V27 N28 V32 L33 S34 E39 F42 R43 E44 A45 V46 N47 Q48 K51 S55 W56 K57 I58 Q59 L60 V65 T66 H67 K68 P69 N70 Q73 Molecule 1: Glutamate receptor ionotropic, NMDA 1 Chain A:

5 Page 5 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH MET SER THR MET ARG THR PHE SER CYS SER VAL ARG CYS ASP K25 I26 V27 N28 V32 L33 S34 E39 F42 R43 E44 A45 V46 N47 Q48 K51 S55 W56 K57 I58 Q59 L60 V65 T66 H67 K68 P69 N70 Q73 M74 A75 L76 S77 V78 C79 E80 D81 S85 S93 H94 P95 P96 T97 P98 T105 S108 Y109 T110 Y114 R115 L119 G120 L121 T122 T123 R124 M125 S126 I127 Y128 H134 L138 R139 T140 V141 P142 P143 Y144 S145 H146 Q147 S148 S149 V150 W151 F152 E153 M154 M155 S159 W160 N161 H162 I163 I164 L165 L166 V167 S168 D169 D170 H171 E172 G173 Q177 K178 R179 L184 A191 E192 K193 V194 L195 Q196 F197 V204 T205 A206 L207 L208 M209 E210 L214 E215 A216 R217 V218 I219 I220 L221 T230 R233 A234 M237 L238 N239 M240 T241 G242 S243 G244 Y245 V246 W247 L248 V249 G250 E251 R252 E253 I254 G265 I266 L267 I272 E277 H280 D283 V287 H293 T302 C308 V309 G310 N311 T312 N313 I314 W315 K316 T317 G318 P319 L320 F321 K322 R323 Y330 G333 V334 T335 V338 E339 F340 N341 G344 D345 R346 K347 N350 Y351 S352 I353 M354 N355 L356 R359 K360 L361 V362 Q363 V364 G365 I366 Y367 N368 H371 V372 I373 P374 N375 D376 R377 K378 I379 I380 W381 G383 G384 G391 T396 R397 L398 K399 I400 V401 T402 I403 H404 Q405 E406 P407 F408 V409 Y410 V411 K412 P413 T414 E423 F424 G428 K432 K433 V434 I435 C436 T437 G438 P439 N440 D441 T442 S446 P447 R448 H449 P452 Q453 C454 C455 Y456 G457 F458 D461 L462 L463 I464 K465 L466 A467 M470 N471 F472 T473 Y474 H477 L478 V479 A480 D481 G482 K483 F484 G485 T486 Q487 E488 R489 V490 N491 N494 K495 K496 E497 W498 N499 G500 M501 M502 G503 E504 L505 L506 S507 G508 Q509 A510 D511 M512 I513 I519 N520 N521 E522 R523 A524 Q525 Y526 I527 E528 F529 S530 K531 K534 Y535 Q536 G537 L538 T539 I540 L541 V542 K543 K544 P547 R548 SER THR ASP S553 F558 Q559 S560 W563 V573 S584 PHE GLY ARG PHE LYS VAL ASN SER GLU GLU GLU GLU GLU ASP L601 S605 A606 M607 W608 F609 S610 L614 L615 G620 E621 G622 ARG S626 F627 I631 L632 G633 W636 T648 L651 L657 D658 ARG GLU GLU R663 N668 R673 K678 F679 A682 T683 V684 K685 Q686 Y692 F693 R694 R695 Q696 V697 Y703 R704 H705 M706 E707 K708 H709 N710 Y711 A715 I718 Q719 A720 D723 N724 K725 L726 H727 A728 F729 I730 W731 A734 V735 L736 E737 F738 E739 A740 S741 Q742 L746 V747 T748 E751 L752 F753 F754 R755 S756 G757 F758 G761 M762 R763 N771 V772 S773 L774 S775 I776 L777 K778 S779 H780 E781 N782 G783 F784 D787 W792 V793 Q796 S802 ASN THR THR F810 E811 N812 M813 A814 G815 V816 F817 V820 I824 I828 I831 R839 R844 ARG LYS GLN Molecule 2: Glutamate receptor ionotropic, NMDA 2A Chain D: MET GLY ARG VAL GLY TYR TRP THR VAL VAL TRP ARG GLY SER GLU LYS GLY L34 N35 I36 A37 V38 M39 L40 G41 H42 S43 H44 D45 R52 P57 D66 V67 N68 V69 V70 A71 L72 L73 R76 T77 D78 P79 K80 S81 L89 I95 H96 G97 L98 V99 F100 G101 D102 Q106 M112 L113 D114 F115 I116 S117 S118 H119 P123 I124 L125 H128 G129 T143 F144 F145 G148 A149 S150 Q153 V157 K160 I161 M162 Q163 D164 Y165 H168 V169 F170 S171 L172 V173 T174 T175 I176 R181 E182 F183 I184 S185 T189 T190 V191 D192 N193 S194 F195 W198 D199 M200 Q201 L206 D207 T208 S209 F210 E211 T215 Q216 V217 Q218 L219 K220 V226 I227 L228 L229 Y230 K233 E242 A243 R244 S245 L246 Y251 F254 W255 I256 V257 P258 S259 L260 V261 T265 K270 P273 S274 G275 L276 I277 S278 V279 S280 Y281 W284 D285 Y286 R291 V292 R293 D294 G295 I298 M306 F310 S311 Y312 E315 Y321 P327 E328 V329 P330 M331 L334 H335 M338 V341 T342 W343 D347 L348 Q356 V357 H358 P359 R360 L361 V362 V363 I364 V365 L366 N367 K368 D369 R370 E373 K374 V375 W378 E379 T382 L383 S384 L385 R386 H387 A388 V389 W390 P391 D398 CYS E400 P401 S407 I408 V409 E413 F416 V417 I418 V419 E420 P424 R431 N432 T433 V434 P435 C436 R437 K438 F439 N443

6 Page 6 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH T446 G449 M450 N451 V452 K453 K454 C455 C456 K457 G458 F459 C460 K466 L467 S468 R469 Y475 D476 L477 Y478 L479 G483 K484 H485 G486 K487 N494 I497 G498 E499 V500 Q503 V506 M507 A508 V509 G510 S511 L512 T513 I514 N515 E516 E517 R518 S519 E520 V521 V522 D523 V526 P527 F528 V529 E530 T531 G532 I533 S534 V535 M536 V537 S538 ARG SER ASN GLY THR VAL SER SER PHE GLU PHE SER A556 S557 V558 M561 I572 E578 Y579 F580 S581 P582 VAL GLY TYR ASN ARG ASN LYS GLY LYS HIS GLY S598 W606 G610 F613 ASN ASN SER VAL VAL GLN ASN LYS GLY T625 T626 I629 M630 V631 S632 V633 W634 A635 F636 F637 F641 L642 A643 S644 Y645 N648 L649 F652 M653 I654 Q655 ARG R657 L665 K668 Q671 R672 P673 F680 R681 F682 G683 T684 N687 T690 E691 R692 N693 I694 R695 N696 N697 Y698 M701 H702 Q703 Y704 M705 Q710 K711 G712 V713 E714 D715 A716 L717 V718 S719 L720 K721 T722 G723 A727 F728 I729 Y730 D731 A732 A733 V734 L735 N736 Y737 K738 A739 G740 R741 K746 L747 V748 T749 I750 G751 S752 G753 Y754 I755 F756 A757 T758 T759 GLY TYR GLY I763 A764 L765 Q766 K767 G768 S769 P770 W771 K772 D776 L777 A778 L779 L780 Q781 G784 D785 E790 L791 E792 T793 L794 W795 L796 I799 C800 S809 SER GLN ASP I814 G819 V820 F821 Y822 M823 L824 A829 L832 F841 Molecule 2: Glutamate receptor ionotropic, NMDA 2A Chain B: MET GLY ARG VAL GLY TYR TRP THR VAL VAL TRP ARG GLY SER GLU LYS GLY L34 N35 I36 A37 V38 M39 L40 G41 H42 S43 H44 D45 R52 P57 D66 V67 N68 V69 V70 A71 L72 L73 T77 D78 P79 K80 S81 L89 I95 H96 G97 L98 V99 F100 G101 D102 Q106 M112 L113 D114 F115 I116 S117 S118 H119 P123 I124 L125 H128 G129 T143 F144 F145 G148 A149 S150 Q153 V157 K160 I161 M162 Q163 D164 Y165 D166 W167 H168 V169 F170 S171 L172 V173 T174 T175 I176 Y180 R181 E182 F183 I184 T189 N193 S194 F195 W198 D199 M200 Q201 L206 D207 T208 S209 F210 E211 T215 Q216 V217 Q218 L219 K220 V226 I227 L228 L229 Y230 K233 E242 A243 R244 S245 L246 Y251 F254 W255 I256 V257 P258 S259 L260 V261 T265 K270 P273 S274 G275 L276 I277 S278 V279 S280 Y281 W284 D285 Y286 R291 V292 R293 D294 G295 I298 F310 S311 Y312 E315 Y321 P327 E328 V329 P330 M331 L334 H335 M338 V341 T342 W343 D347 L348 Q356 V357 H358 P359 R360 L361 V362 V363 I364 V365 L366 N367 K368 D369 R370 E373 K374 V375 W378 E379 T382 L383 S384 L385 R386 H387 A388 V389 W390 P391 D398 CYS E400 P401 S407 I408 V409 E413 F416 V417 I418 V419 E420 P424 R431 N432 T433 V434 P435 C436 R437 K438 F439 N443 T446 G449 M450 N451 V452 K453 K454 C455 C456 K457 G458 F459 C460 I461 K466 L467 S468 R469 Y475 D476 L477 Y478 L479 G483 K484 H485 G486 K487 N494 I497 G498 E499 V500 Q503 V506 M507 A508 V509 G510 S511 L512 T513 I514 N515 E516 E517 R518 S519 E520 V521 V522 D523 V526 P527 F528 V529 E530 I533 S534 V535 M536 V537 S538 ARG SER ASN GLY THR VAL SER SER PHE GLU PHE SER A556 S557 V558 M561 I572 Y579 P582 VAL GLY TYR ASN ARG ASN LYS GLY LYS HIS GLY S598 W606 G610 F613 ASN ASN SER VAL VAL GLN ASN LYS GLY T625 T626 I629 M630 V631 S632 V633 W634 A635 F636 F637 F641 L642 A643 S644 Y645 N648 L649 F652 M653 I654 Q655 ARG R657 L665 K668 Q671 R672 P673 F680 R681 F682 G683 T684 T690 E691 R692 N693 I694 R695 N696 N697 Y698 M701 H702 Q703 Y704 M705 Q710 K711 G712 V713 E714 D715 A716 L717 V718 S719 L720 K721 T722 G723 K724 L725 D726 A727 F728 I729 Y730 D731 A732 A733 V734 L735 N736 Y737 K738 A739 G740 R741 K746 L747 V748 T749 I750 G751 S752 G753 F756 A757 T758 T759 GLY TYR GLY I763 A764 L765 Q766 K767 G768 S769 P770 W771 K772 D776 L777 A778 L779 L780 Q781 G784 D785 E790 L791 E792 T793 L794 W795 L796 I799 C800 S809 SER GLN ASP I814 G819 V820 F821 Y822 M823 L824 A829 L832 F841

7 Page 7 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 4 Experimental information i Property Value Source Reconstruction method SINGLE PARTICLE Depositor Imposed symmetry POINT, Not provided Depositor Number of particles used Depositor Resolution determination method FSC CUT-OFF Depositor CTF correction method PHASE FLIPPING AND AMPLITUDE Depositor CORRECTION Microscope FEI TITAN KRIOS Depositor Voltage (kv) 300 Depositor Electron dose (e /Å 2 ) 56 Depositor Minimum defocus (nm) Not provided Depositor Maximum defocus (nm) Not provided Depositor Magnification Not provided Depositor Image detector GATAN K2 SUMMIT (4k x 4k) Depositor

8 Page 8 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 5 Model quality i 5.1 Standard geometry 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). Mol Chain Bond lengths Bond angles RMSZ # Z >2 RMSZ # Z >2 1 A / /8483 (0.1%) 1 C / /8498 (0.1%) 2 B /5946 (0.0%) /8072 (0.1%) 2 D /5946 (0.0%) /8072 (0.1%) All All /24447 (0.0%) /33125 (0.1%) 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 A C B D 0 6 All All 0 23 All (3) bond length outliers are listed below: Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 2 B 536 MET C-N D 343 TRP CB-CG B 343 TRP CB-CG All (40) bond angle outliers are listed below: Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 1 C 95 N-CA-CB A 95 N-CA-CB D 327 N-CA-CB B 327 N-CA-CB C 184 CA-CB-CG

9 Page 9 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 1 A 184 CA-CB-CG D 424 N-CA-CB B 424 N-CA-CB D 529 VAL C-N-CA D 391 N-CA-CB B 391 N-CA-CB B 529 VAL C-N-CA C 777 O-C-N A 777 O-C-N C 547 N-CA-CB A 547 N-CA-CB D 401 N-CA-CB B 401 N-CA-CB D 727 O-C-N A 169 ASP CB-CG-OD C 169 ASP CB-CG-OD A 96 N-CA-CB C 96 N-CA-CB D 330 N-CA-CB B 330 N-CA-CB A 98 N-CA-CB C 98 N-CA-CB C 777 CA-C-N A 777 CA-C-N B 57 N-CA-CB D 57 N-CA-CB B 343 TRP CA-CB-CG D 343 TRP CA-CB-CG D 729 ILE O-C-N B 176 ILE CG1-CB-CG D 176 ILE CG1-CB-CG A 254 ILE CG1-CB-CG C 254 ILE CG1-CB-CG A 238 C-N-CA C 238 C-N-CA There are no chirality outliers. All (23) planarity outliers are listed below: Mol Chain Res Type Group 1 A 162 HIS Peptide 1 A 248 Peptide

10 Page 10 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH Mol Chain Res Type Group 1 A 353 ILE Peptide 1 A 368 ASN Peptide 1 A 491 ASN Peptide 2 B 170 PHE Peptide 2 B 251 TYR Peptide 2 B 310 PHE Peptide 2 B 331 MET Peptide 2 B 44 HIS Peptide 2 B 796 Peptide 1 C 162 HIS Peptide 1 C 248 Peptide 1 C 353 ILE Peptide 1 C 368 ASN Peptide 1 C 381 TRP Peptide 1 C 491 ASN Peptide 2 D 170 PHE Peptide 2 D 251 TYR Peptide 2 D 310 PHE Peptide 2 D 331 MET Peptide 2 D 44 HIS Peptide 2 D 796 Peptide 5.2 Too-close contacts 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 C B D All All The all-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The all-atom clashscore for this structure is 36. All (1715) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude.

11 Page 11 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:B:416:PHE:CE1 2:B:528:PHE:CE :B:416:PHE:CD1 2:B:528:PHE:CZ :B:416:PHE:CD1 2:B:528:PHE:HZ :A:56:TRP:CB 1:A:59:GLN:HG :C:56:TRP:CB 1:C:59:GLN:CG :D:534:SER:HB3 2:D:750:ILE:CG :B:526:VAL:HG21 2:B:779::CD :D:582::CG 1:A:839:ARG:HH :A:56:TRP:CB 1:A:59:GLN:CG :D:416:PHE:CD1 2:D:528:PHE:HZ :D:526:VAL:HG21 2:D:779::CD :C:839:ARG:HH22 2:B:582::CG :D:416:PHE:CD1 2:D:528:PHE:CZ :D:416:PHE:CE1 2:D:528:PHE:CE :C:56:TRP:CB 1:C:59:GLN:HG :B:534:SER:HB3 2:B:750:ILE:CG :B:537:VAL:CG1 2:B:727::CB :C:817:PHE:CZ 2:B:561:MET:HB :D:416:PHE:CZ 2:D:528:PHE:HE :D:561:MET:HB3 1:A:817:PHE:CZ :D:534:SER:CB 2:D:750:ILE:HG :C:521:ASN:CG 2:B:780::HB :B:537:VAL:HG12 2:B:727::CB :B:416:PHE:CZ 2:B:528:PHE:HE :B:534:SER:CB 2:B:750:ILE:HG :C:521:ASN:ND2 2:B:780::CB :D:526:VAL:CG2 2:D:779::HD :B:526:VAL:CG2 2:B:779::HD :D:780::CB 1:A:521:ASN:ND :D:780::HB3 1:A:521:ASN:ND :B:537:VAL:CG1 2:B:727::HB :C:839:ARG:NH2 2:B:582::HG :D:582::HG2 1:A:839:ARG:NH :D:629:ILE:HD11 1:A:608:TRP:CE :B:630:MET:O 2:B:634:TRP:CE :D:780::HB3 1:A:521:ASN:CG :C:531:LYS:CB 1:C:776:ILE:HD :C:521:ASN:ND2 2:B:780::HB :C:608:TRP:CE2 2:B:629:ILE:HD :D:634:TRP:CZ2 1:A:824:ILE:CG :D:533:ILE:O 2:D:756:PHE:N :B:533:ILE:O 2:B:756:PHE:N

12 Page 12 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1:C:824:ILE:CG1 2:B:634:TRP:CZ :A:531:LYS:CB 1:A:776:ILE:HD :D:777::HA 1:A:521:ASN:OD :D:630:MET:O 2:D:634:TRP:CE :D:526:VAL:CG2 2:D:779::CD :B:536:MET:O 2:B:728:PHE:N :D:629:ILE:CD1 1:A:608:TRP:CE :C:608:TRP:CE2 2:B:629:ILE:CD :A:56:TRP:CB 1:A:59:GLN:CD :D:784:GLY:O 1:A:696:GLN:NE :C:696:GLN:NE2 2:B:784:GLY:O :D:526:VAL:CG1 2:D:527::HD :C:56:TRP:CB 1:C:59:GLN:CD :B:526:VAL:CG1 2:B:527::HD :C:820:VAL:HG13 2:B:634:TRP:NE :C:817:PHE:CZ 2:B:561:MET:CB :D:634:TRP:CZ2 1:A:824:ILE:HG :B:526:VAL:HG12 2:B:527::CD :C:521:ASN:OD1 2:B:777::HA :D:645:TYR:OH 1:A:810:PHE:HE :C:810:PHE:HE2 2:B:645:TYR:OH :A:773:SER:O 1:A:776:ILE:HG :D:526:VAL:HG12 2:D:527::CD :B:526:VAL:CG2 2:B:779::CD :C:521:ASN:HB2 2:B:780::CG :C:531:LYS:HB2 1:C:776:ILE:CD :D:561:MET:CB 1:A:817:PHE:CZ :C:233:ARG:O 1:C:237:MET:HG :A:233:ARG:O 1:A:237:MET:HG :A:531:LYS:HB2 1:A:776:ILE:CD :D:536:MET:O 2:D:728:PHE:N :D:634:TRP:NE1 1:A:820:VAL:HG :D:537:VAL:O 2:D:748:VAL:N :B:537:VAL:O 2:B:748:VAL:N :C:535:TYR:CE2 2:B:759:THR:HG :C:773:SER:O 1:C:776:ILE:HG :C:521:ASN:CG 2:B:780::CB :D:561:MET:HB3 1:A:817:PHE:CE :B:534:SER:O 2:B:729:ILE:HG :D:534:SER:O 2:D:729:ILE:HG :C:817:PHE:CE1 2:B:561:MET:HB

13 Page 13 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:D:629:ILE:HD11 1:A:608:TRP:CD :D:780::CB 1:A:521:ASN:CG :D:629:ILE:HD13 1:A:608:TRP:NE :C:608:TRP:NE1 2:B:629:ILE:HD :C:521:ASN:HB2 2:B:780::CD :D:516:GLU:HG2 1:A:777::CD :C:824:ILE:HG12 2:B:634:TRP:CZ :B:416:PHE:CE1 2:B:528:PHE:CZ :C:777::CD1 2:B:516:GLU:HG :D:537:VAL:N 2:D:748:VAL:O :B:537:VAL:O 2:B:748:VAL:O :C:535:TYR:HE2 2:B:759:THR:CG :D:537:VAL:O 2:D:748:VAL:O :D:416:PHE:CE1 2:D:528:PHE:CZ :B:537:VAL:CG1 2:B:727::HB :C:839:ARG:CZ 2:B:582::HB :B:537:VAL:N 2:B:748:VAL:O :C:608:TRP:CD2 2:B:629:ILE:HD :D:416:PHE:CZ 2:D:528:PHE:CE :B:416:PHE:CZ 2:B:528:PHE:CE :D:538:SER:HA 2:D:747::HA :D:759:THR:HG22 1:A:535:TYR:CE :D:780::CD2 1:A:521:ASN:HB :C:521:ASN:CB 2:B:780::CB :C:521:ASN:CB 2:B:780::HB :D:759:THR:HG21 1:A:780:HIS:CE :A:773:SER:O 1:A:776:ILE:CG :C:773:SER:O 1:C:776:ILE:CG :C:816:VAL:HG11 2:B:641:PHE:CZ :B:534:SER:O 2:B:729:ILE:HA :C:813:MET:CE 2:B:558:VAL:HG :D:780::HB3 1:A:521:ASN:CB :B:534:SER:O 2:B:729:ILE:CG :D:780::CB 1:A:521:ASN:CB :D:641:PHE:CZ 1:A:816:VAL:HG :C:780:HIS:CE1 2:B:759:THR:HG :D:759:THR:CG2 1:A:535:TYR:HE :D:780::CG 1:A:521:ASN:HB :D:558:VAL:HG13 1:A:813:MET:CE :C:777::HB3 2:B:516:GLU:HB :D:582::HB2 1:A:839:ARG:CZ

14 Page 14 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:D:558:VAL:HG13 1:A:813:MET:HE :D:534:SER:O 2:D:729:ILE:HA :D:634:TRP:CZ2 1:A:824:ILE:HG :C:777::HD12 2:B:516:GLU:HG :C:773:SER:O 1:C:777::HG :D:216:GLN:O 2:B:220:LYS:NZ :B:534:SER:CB 2:B:732::HB :A:208::HB3 1:A:238::HD :C:208::HB3 1:C:238::HD :B:538:SER:HA 2:B:747::HA :A:26:ILE:HG12 1:A:58:ILE:HG :D:534:SER:CB 2:D:732::HB :C:839:ARG:NH2 2:B:582::CB :A:773:SER:O 1:A:777::HG :B:526:VAL:HG21 2:B:779::HD :D:534:SER:HB3 2:D:750:ILE:HG :C:520:ASN:HD22 1:C:523:ARG:CG :D:220:LYS:NZ 2:B:216:GLN:O :C:824:ILE:HG13 2:B:634:TRP:CZ :D:534:SER:O 2:D:729:ILE:CG :D:516:GLU:HG2 1:A:777::HD :A:520:ASN:HD22 1:A:523:ARG:CG :D:537:VAL:HG23 2:D:748:VAL:HB :B:534:SER:O 2:B:729:ILE:CA :B:533:ILE:O 2:B:756:PHE:CA :C:26:ILE:HG12 1:C:58:ILE:O :C:521:ASN:HB2 2:B:780::CB :C:817:PHE:HZ 2:B:561:MET:CB :C:521:ASN:ND2 2:B:780::CA :D:516:GLU:HB2 1:A:777::HB :A:520:ASN:HD22 1:A:523:ARG:HG :D:533:ILE:O 2:D:756:PHE:CA :B:537:VAL:HG23 2:B:748:VAL:HB :D:526:VAL:HG21 2:D:779::HD :B:537:VAL:HG13 2:B:727::HB :C:839:ARG:NH2 2:B:582::CG :C:520:ASN:HD22 1:C:523:ARG:HG :C:813:MET:HE2 2:B:558:VAL:HG :D:780::CB 1:A:521:ASN:HB :C:521:ASN:HB2 2:B:780::HD :D:582::CB 1:A:839:ARG:NH

15 Page 15 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1:A:26:ILE:HG12 1:A:58:ILE:O :A:520:ASN:ND2 1:A:523:ARG:CD :C:820:VAL:HG13 2:B:634:TRP:HE :C:520:ASN:ND2 1:C:523:ARG:CD :C:26:ILE:HG12 1:C:58:ILE:HG :C:648:THR:HG22 2:B:643::HB :D:561:MET:CB 1:A:817:PHE:HZ :D:534:SER:O 2:D:729:ILE:CA :A:233:ARG:O 1:A:237:MET:CG :B:534:SER:HB3 2:B:750:ILE:HG :B:534:SER:OG 2:B:732::HB :C:242:GLY:O 1:C:245:TYR:HD :A:242:GLY:O 1:A:245:TYR:HD :D:634:TRP:HE1 1:A:820:VAL:HG :D:643::HB1 1:A:648:THR:HG :A:519:ILE:HG23 1:A:529:PHE:CE :C:820:VAL:CG1 2:B:634:TRP:HE :D:582::CG 1:A:839:ARG:NH :D:780::CA 1:A:521:ASN:ND :D:630:MET:HB3 2:D:634:TRP:HZ :C:519:ILE:HG23 1:C:529:PHE:CE :B:630:MET:HB3 2:B:634:TRP:HZ :C:233:ARG:O 1:C:237:MET:CG :D:629:ILE:CD1 1:A:608:TRP:NE :D:534:SER:OG 2:D:732::HB :D:780::HD22 1:A:521:ASN:HB :C:777::CD1 2:B:516:GLU:CG :D:416:PHE:CG 2:D:528:PHE:HZ :D:534:SER:HB2 2:D:732::HB :A:531:LYS:NZ 1:A:777::HD :C:608:TRP:NE1 2:B:629:ILE:CD :C:531:LYS:NZ 1:C:777::HD :D:516:GLU:HA 1:A:777::HD :D:634:TRP:HE1 1:A:820:VAL:CG :B:416:PHE:CG 2:B:528:PHE:HZ :D:777::CA 1:A:521:ASN:OD :D:634:TRP:HZ2 1:A:824:ILE:HG :C:777::HD12 2:B:516:GLU:CG :D:536:MET:HA 2:D:749:THR:HA :A:520:ASN:HD22 1:A:523:ARG:CD :C:777::HD13 2:B:516:GLU:HA

16 Page 16 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:B:534:SER:O 2:B:729:ILE:CB :C:521:ASN:OD1 2:B:777::CA :A:531:LYS:HD2 1:A:776:ILE:HG :C:531:LYS:HD2 1:C:776:ILE:HG :D:516:GLU:CG 1:A:777::CD :C:820:VAL:CG1 2:B:634:TRP:NE :B:534:SER:HB2 2:B:732::HB :A:466::O 1:A:470:MET:HB :C:520:ASN:HD22 1:C:523:ARG:CD :D:438:LYS:O 2:D:451:ASN:HA :C:466::O 1:C:470:MET:HB :C:824:ILE:HG13 2:B:634:TRP:HZ :B:630:MET:O 2:B:634:TRP:CZ :D:630:MET:O 2:D:634:TRP:CZ :C:651::HD12 2:B:643::HB :C:773:SER:C 1:C:776:ILE:HG :B:438:LYS:O 2:B:451:ASN:HA :D:534:SER:O 2:D:729:ILE:CB :B:460:CYS:SG 2:B:528:PHE:HE :C:648:THR:HG22 2:B:643::CB :A:234::O 1:A:237:MET:HB :C:820:VAL:HG13 2:B:634:TRP:CD :C:234::O 1:C:237:MET:HB :A:773:SER:C 1:A:776:ILE:HG :D:538:SER:C 2:D:748:VAL:HG :D:634:TRP:NE1 1:A:820:VAL:CG :A:531:LYS:O 1:A:776:ILE:HD :C:531:LYS:O 1:C:776:ILE:HD :A:242:GLY:O 1:A:245:TYR:CD :D:516:GLU:CG 1:A:777::HD :D:537:VAL:O 2:D:747::C :B:538:SER:C 2:B:748:VAL:HG :D:460:CYS:SG 2:D:528:PHE:HE :B:534:SER:CB 2:B:750:ILE:CG :C:777::HD13 2:B:516:GLU:CB :C:242:GLY:O 1:C:245:TYR:CD :B:537:VAL:O 2:B:747::C :D:643::CB 1:A:648:THR:HG :B:630:MET:O 2:B:634:TRP:HE :C:26:ILE:CG1 1:C:58:ILE:O :D:416:PHE:CG 2:D:528:PHE:CZ

17 Page 17 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:D:534:SER:CB 2:D:750:ILE:CG :D:643::HB1 1:A:651::HD :D:634:TRP:CD1 1:A:820:VAL:HG :D:759:THR:HG22 1:A:535:TYR:HE :D:629:ILE:HD13 1:A:608:TRP:CD :C:817:PHE:CE2 2:B:561:MET:HE :A:520:ASN:ND2 1:A:523:ARG:HD :C:608:TRP:CD1 2:B:629:ILE:HD :C:520:ASN:ND2 1:C:523:ARG:HD :A:26:ILE:CG1 1:A:58:ILE:O :A:531:LYS:NZ 1:A:777::HD :C:521:ASN:CG 2:B:780::HB :C:824:ILE:HD11 2:B:634:TRP:CE :B:630:MET:HB3 2:B:634:TRP:CZ :C:608:TRP:CH2 2:B:626:THR:HG :D:634:TRP:CH2 1:A:824:ILE:HG :B:533:ILE:HB 2:B:757::N :D:533:ILE:CG2 2:D:729:ILE:CG :D:630:MET:O 2:D:634:TRP:HE :B:534:SER:OG 2:B:732::CB :C:531:LYS:NZ 1:C:777::HD :D:634:TRP:CE2 1:A:824:ILE:HD :D:641:PHE:HZ 1:A:816:VAL:HG :C:535:TYR:CE2 2:B:759:THR:CG :D:516:GLU:CB 1:A:777::HD :C:520:ASN:HB2 1:C:523:ARG:HB :C:777::HD13 2:B:516:GLU:CA :B:533:ILE:HG22 2:B:729:ILE:CG :C:824:ILE:HG12 2:B:634:TRP:CH :B:534:SER:HB3 2:B:750:ILE:HG :C:817:PHE:CD2 2:B:561:MET:HE :D:630:MET:HB3 2:D:634:TRP:CZ :C:820:VAL:CG1 2:B:634:TRP:CD :C:816:VAL:HG11 2:B:641:PHE:HZ :A:520:ASN:HB2 1:A:523:ARG:HB :B:416:PHE:CG 2:B:528:PHE:CZ :C:26:ILE:CG1 1:C:58:ILE:HG :D:526:VAL:HG21 2:D:779::HD :B:533:ILE:CG2 2:B:729:ILE:CG :D:533:ILE:HG22 2:D:729:ILE:CG :C:531:LYS:HZ3 1:C:777::HD

18 Page 18 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1:A:531:LYS:HZ2 1:A:777::HD :B:526:VAL:HG21 2:B:779::HD :A:519:ILE:HG12 1:A:529:PHE:CE :D:626:THR:HG22 1:A:608:TRP:CH :A:26:ILE:CG1 1:A:58:ILE:HG :C:816:VAL:CG1 2:B:641:PHE:HZ :A:531:LYS:HZ3 1:A:777::HD :D:558:VAL:CG1 1:A:813:MET:HE :C:521:ASN:HD22 2:B:780::CB :B:536:MET:HA 2:B:749:THR:HA :C:519:ILE:HG12 1:C:529:PHE:CE :D:534:SER:OG 2:D:732::CB :C:531:LYS:O 1:C:776:ILE:CD :A:531:LYS:O 1:A:776:ILE:CD :D:533:ILE:HB 2:D:757::N :D:759:THR:CG2 1:A:780:HIS:CE :C:521:ASN:ND2 2:B:780::N :D:561:MET:HE2 1:A:817:PHE:CE :B:537:VAL:O 2:B:748:VAL:C :A:208::CB 1:A:238::HD :C:780:HIS:CE1 2:B:759:THR:CG :C:520:ASN:ND2 1:C:523:ARG:HG :D:561:MET:HE2 1:A:817:PHE:CD :D:516:GLU:CA 1:A:777::HD :C:208::CB 1:C:238::HD :D:538:SER:C 2:D:748:VAL:H :A:540:ILE:O 1:A:748:THR:HA :C:56:TRP:CB 1:C:59:GLN:CB :D:537:VAL:O 2:D:748:VAL:C :D:433:THR:HA 2:D:456:CYS:O :D:534:SER:HB3 2:D:750:ILE:HG :D:536:MET:HA 2:D:749:THR:CA :A:56:TRP:CB 1:A:59:GLN:CB :D:641:PHE:HZ 1:A:816:VAL:CG :D:536:MET:O 2:D:727::C :B:433:THR:HA 2:B:456:CYS:O :A:520:ASN:ND2 1:A:523:ARG:HG :C:540:ILE:O 1:C:748:THR:HA :D:516:GLU:HB2 1:A:777::CB :D:777::O 1:A:521:ASN:ND :D:634:TRP:CD1 1:A:820:VAL:CG

19 Page 19 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:B:538:SER:C 2:B:748:VAL:H :C:531:LYS:CB 1:C:776:ILE:CD :C:531:LYS:HZ2 1:C:777::HD :C:816:VAL:CG1 2:B:641:PHE:CZ :B:537:VAL:C 2:B:748:VAL:O :C:519:ILE:HG12 1:C:529:PHE:CZ :C:813:MET:HE1 2:B:558:VAL:HG :B:534:SER:CB 2:B:732::CB :D:558:VAL:CG1 1:A:813:MET:CE :A:208::HB3 1:A:238::CD :D:759:THR:CG2 1:A:535:TYR:CE :B:538:SER:HA 2:B:747::CA :B:780::O 2:B:784:GLY:N :D:534:SER:CB 2:D:732::CB :B:536:MET:HB2 2:B:735::HD :A:519:ILE:HG12 1:A:529:PHE:CZ :C:777::CB 2:B:516:GLU:HB :C:813:MET:CE 2:B:558:VAL:CG :A:520:ASN:ND2 1:A:523:ARG:CG :D:538:SER:HA 2:D:747::CA :D:780::HB3 1:A:521:ASN:HB :C:164:ILE:HB 1:C:218:VAL:O :C:536:GLN:O 1:C:755:ARG:HA :D:780::N 1:A:521:ASN:ND :D:780::O 2:D:784:GLY:N :A:536:GLN:O 1:A:755:ARG:HA :D:537:VAL:C 2:D:748:VAL:O :D:641:PHE:CZ 1:A:816:VAL:CG :D:115:PHE:O 2:D:119:HIS:HB :B:115:PHE:O 2:B:119:HIS:HB :C:839:ARG:CZ 2:B:582::CB :A:164:ILE:HB 1:A:218:VAL:O :B:537:VAL:O 2:B:748:VAL:CA :D:780::HB2 1:A:521:ASN:CG :A:76::O 1:A:80:GLU:HB :C:521:ASN:CB 2:B:780::HD :D:759:THR:HG21 1:A:780:HIS:HE :B:460:CYS:SG 2:B:528:PHE:CE :C:777::HD13 2:B:516:GLU:HG :C:76::O 1:C:80:GLU:HB :D:582::CB 1:A:839:ARG:CZ

20 Page 20 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:D:537:VAL:O 2:D:748:VAL:CA :A:144:TYR:O 1:A:147:GLN:HB :A:531:LYS:CB 1:A:776:ILE:CD :C:813:MET:HE1 2:B:558:VAL:CG :C:839:ARG:NH1 2:B:582::HB :C:817:PHE:HZ 2:B:561:MET:HB :D:780::HD22 1:A:521:ASN:CB :C:144:TYR:O 1:C:147:GLN:HB :D:534:SER:HB2 2:D:732::CB :D:460:CYS:SG 2:D:528:PHE:CE :B:534:SER:HB2 2:B:732::CB :B:435::HA 2:B:454:LYS:O :B:751:GLY:O 2:B:753:GLY:N :C:780:HIS:CG 2:B:759:THR:HG :D:516:GLU:HG2 1:A:777::HD :D:780::HB3 1:A:521:ASN:HD :C:521:ASN:HD22 2:B:780::HB :D:634:TRP:CE2 1:A:824:ILE:CG :D:751:GLY:O 2:D:753:GLY:N :C:521:ASN:ND2 2:B:777::O :D:435::HA 2:D:454:LYS:O :B:535:VAL:HA 2:B:729:ILE:CA :C:777::HB2 2:B:516:GLU:HG :D:516:GLU:HG3 1:A:777::HB :C:208::HB3 1:C:238::CD :C:817:PHE:CZ 2:B:561:MET:HE :D:536:MET:HB2 2:D:735::HD :B:537:VAL:CA 2:B:748:VAL:O :D:561:MET:CG 1:A:817:PHE:CZ :D:636:PHE:HB2 1:A:615::HD :D:536:MET:O 2:D:727::CA :C:233:ARG:C 1:C:237:MET:HG :D:537:VAL:CA 2:D:748:VAL:O :C:521:ASN:HD21 2:B:780::N :D:561:MET:HE3 1:A:817:PHE:CD :C:817:PHE:CZ 2:B:561:MET:CG :D:533:ILE:HG22 2:D:729:ILE:HG :C:839:ARG:NH2 2:B:582::HB :B:534:SER:C 2:B:729:ILE:HG :B:533:ILE:HG22 2:B:729:ILE:HG :A:233:ARG:C 1:A:237:MET:HG

21 Page 21 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:D:582::HB2 1:A:839:ARG:NH :C:615::HD22 2:B:636:PHE:HB :C:824:ILE:CG1 2:B:634:TRP:CE :A:520:ASN:ND2 1:A:523:ARG:NE :C:695:ARG:HH22 2:B:780::CD :C:520:ASN:ND2 1:C:523:ARG:NE :C:77:SER:O 1:C:81:ASP:HB :D:561:MET:HE3 1:A:817:PHE:CE :C:520:ASN:HB2 1:C:523:ARG:CB :B:535:VAL:HA 2:B:729:ILE:HA :C:695:ARG:HH22 2:B:780::HD :C:780:HIS:HE1 2:B:759:THR:HG :A:77:SER:O 1:A:81:ASP:HB :D:516:GLU:CG 1:A:777::HD :C:519:ILE:HG12 1:C:529:PHE:CD :D:416:PHE:CD1 2:D:528:PHE:CE :A:520:ASN:HB2 1:A:523:ARG:CB :D:561:MET:HB2 1:A:817:PHE:HZ :B:265:THR:HG1 2:B:284:TRP:HE :C:521:ASN:ND2 2:B:781:GLN:H :C:777::HD13 2:B:516:GLU:CG :C:651::CD1 2:B:643::HB :A:519:ILE:HG12 1:A:529:PHE:CD :D:117:SER:HB2 2:D:143:THR:H :D:780::CB 1:A:521:ASN:HD :C:26:ILE:HD11 1:C:58:ILE:HG :D:561:MET:CE 1:A:817:PHE:CE :C:521:ASN:HD22 2:B:781:GLN:N :D:780::CD1 1:A:695:ARG:HH :B:117:SER:HB2 2:B:143:THR:H :C:521:ASN:ND2 2:B:781:GLN:N :C:438:GLY:HA3 1:C:478::HB :A:540:ILE:HA 1:A:729:PHE:O :A:26:ILE:HD11 1:A:58:ILE:HG :D:629:ILE:CD1 1:A:608:TRP:CZ :C:510::O 1:C:763:ARG:NH :D:759:THR:HG1 1:A:780:HIS:CG :D:781:GLN:N 1:A:521:ASN:HD :D:781:GLN:H 1:A:521:ASN:ND :D:561:MET:CE 1:A:817:PHE:CD :D:533:ILE:HG23 2:D:729:ILE:HG

22 Page 22 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1:C:817:PHE:CD1 2:B:561:MET:CE :A:510::O 1:A:763:ARG:NH :D:780::N 1:A:521:ASN:HD :C:540:ILE:HA 1:C:729:PHE:O :D:626:THR:HG22 1:A:608:TRP:HH :D:780::HD11 1:A:695:ARG:HH :D:534:SER:C 2:D:729:ILE:HG :A:438:GLY:HA3 1:A:478::HB :B:432:ASN:HB2 2:B:457:LYS:HE :C:839:ARG:HH21 2:B:582::HG :C:535:TYR:HE2 2:B:759:THR:HG :C:817:PHE:CE1 2:B:561:MET:CE :C:608:TRP:CD1 2:B:629:ILE:CD :D:634:TRP:NE1 1:A:824:ILE:HD :D:643::HB1 1:A:651::CD :B:533:ILE:HG23 2:B:729:ILE:HG :D:781:GLN:N 1:A:521:ASN:ND :B:413:GLU:H 2:B:417:VAL:HB :C:535:TYR:CD2 2:B:759:THR:HG :C:531:LYS:HD2 1:C:776:ILE:CG :D:558:VAL:HG13 1:A:813:MET:HE :D:413:GLU:H 2:D:417:VAL:HB :C:817:PHE:CD1 2:B:561:MET:HE :D:533:ILE:O 2:D:756:PHE:C :D:634:TRP:CE2 1:A:824:ILE:CD :C:25:LYS:HB3 1:C:59:GLN:HG :D:759:THR:HG21 1:A:535:TYR:HE :B:416:PHE:CD1 2:B:528:PHE:CE :D:582::HG2 1:A:839:ARG:HH :C:26:ILE:CD1 1:C:58:ILE:CG :A:520:ASN:CB 1:A:523:ARG:H :D:630:MET:CB 2:D:634:TRP:HZ :D:561:MET:HE2 1:A:817:PHE:CZ :B:536:MET:HA 2:B:749:THR:CA :D:432:ASN:HB2 2:D:457:LYS:HE :C:520:ASN:CB 1:C:523:ARG:H :A:25:LYS:HB3 1:A:59:GLN:HG :D:629:ILE:CD1 1:A:608:TRP:CD :B:630:MET:CB 2:B:634:TRP:HZ :A:56:TRP:CB 1:A:59:GLN:NE :D:36:ILE:O 2:D:69:VAL:HA

23 Page 23 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1:A:26:ILE:CD1 1:A:58:ILE:CG :B:416:PHE:HA 2:B:459:PHE:HB :C:26:ILE:HD11 1:C:58:ILE:CG :D:572:ILE:HD13 1:A:828:ILE:HD :B:407:SER:HA 2:B:476:ASP:HB :C:519:ILE:HG12 1:C:529:PHE:CE :A:531:LYS:HD2 1:A:776:ILE:CG :B:765::HD13 2:B:772:LYS:HG :C:608:TRP:CZ2 2:B:629:ILE:CD :D:416:PHE:HA 2:D:459:PHE:HB :A:520:ASN:HB2 1:A:523:ARG:H :A:521:ASN:O 1:A:525:GLN:HG :C:824:ILE:HD11 2:B:634:TRP:NE :C:824:ILE:CD1 2:B:634:TRP:CE :B:536:MET:O 2:B:727::CA :B:769:SER:HB2 2:B:771:TRP:HD :C:608:TRP:HH2 2:B:626:THR:HG :D:407:SER:HA 2:D:476:ASP:HB :C:775:SER:C 1:C:777::H :B:36:ILE:O 2:B:69:VAL:HA :B:536:MET:C 2:B:728:PHE:H :C:810:PHE:HE2 2:B:645:TYR:CZ :C:521:ASN:O 1:C:525:GLN:HG :D:416:PHE:CE2 2:D:528:PHE:HE :A:519:ILE:HG12 1:A:529:PHE:CE :B:161:ILE:HA 2:B:386:ARG:HH :B:416:PHE:CE2 2:B:528:PHE:HE :C:520:ASN:HB2 1:C:523:ARG:H :D:759:THR:HG22 1:A:535:TYR:CD :A:775:SER:C 1:A:777::H :C:839:ARG:NH2 2:B:582::O :D:161:ILE:HA 2:D:386:ARG:HH :D:750:ILE:HG12 2:D:750:ILE:O :C:56:TRP:CB 1:C:59:GLN:NE :B:682:PHE:HE1 2:B:727::HB :B:533:ILE:N 2:B:757::HB :D:765::HD13 2:D:772:LYS:HG :A:410:TYR:HB2 1:A:456:TYR:HB :D:769:SER:HB2 2:D:771:TRP:HD :C:521:ASN:HB2 2:B:780::HB :C:696:GLN:HE21 2:B:784:GLY:C

24 Page 24 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1:C:410:TYR:HB2 1:C:456:TYR:HB :D:265:THR:HG1 2:D:284:TRP:HE :A:531:LYS:C 1:A:776:ILE:HD :B:750:ILE:HG12 2:B:750:ILE:O :D:280:SER:O 2:D:362:VAL:HB :A:302:THR:HG21 1:A:316:LYS:HB :B:526:VAL:CG2 2:B:779::HD :C:531:LYS:C 1:C:776:ILE:HD :D:270:LYS:O 2:D:370:ARG:NH :A:26:ILE:HD11 1:A:58:ILE:CG :B:280:SER:O 2:B:362:VAL:HB :B:270:LYS:O 2:B:370:ARG:NH :C:828:ILE:HD11 2:B:572:ILE:HD :D:629:ILE:HD11 1:A:608:TRP:CZ :D:343:TRP:HB2 2:D:348::HD :D:526:VAL:CG2 2:D:779::HD :D:582::CG 1:A:839:ARG:CZ :D:759:THR:OG1 1:A:780:HIS:CG :B:416:PHE:HD1 2:B:528:PHE:CZ :C:777::CD1 2:B:516:GLU:CB :D:536:MET:O 2:D:727::HB :B:534:SER:HB2 2:B:750:ILE:HG :B:36:ILE:HB 2:B:69:VAL:HG :B:776:ASP:O 2:B:779::HB :C:521:ASN:ND2 2:B:780::H :C:651::CD1 2:B:643::CB :C:28:ASN:ND2 1:C:85:SER:O :C:302:THR:HG21 1:C:316:LYS:HB :D:36:ILE:HB 2:D:69:VAL:HG :D:526:VAL:HG22 2:D:779::CD :C:817:PHE:CE1 2:B:561:MET:HE :D:516:GLU:CB 1:A:777::HB :B:486:GLY:O 2:B:692:ARG:NH :C:558:PHE:HA 2:D:814:ILE:HG :A:433:LYS:HA 1:A:455:CYS:O :A:531:LYS:HZ2 1:A:777::CD :C:351:TYR:O 1:C:366:ILE:HA :B:343:TRP:HB2 2:B:348::HD :C:26:ILE:CD1 1:C:58:ILE:HG :D:537:VAL:HA 2:D:727::HA :C:780:HIS:CG 2:B:759:THR:OG

25 Page 25 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:D:582::O 1:A:839:ARG:NH :B:533:ILE:CG2 2:B:729:ILE:HG :C:220:ILE:HA 1:C:248::HB :C:433:LYS:HA 1:C:455:CYS:O :D:486:GLY:O 2:D:692:ARG:NH :D:533:ILE:N 2:D:757::HB :D:776:ASP:O 2:D:779::HB :C:534:LYS:O 1:C:757:GLY:HA :D:665::O 2:D:671:GLN:NE :A:351:TYR:O 1:A:366:ILE:HA :B:533:ILE:O 2:B:756:PHE:CB :D:537:VAL:HG23 2:D:748:VAL:CB :D:533:ILE:CG2 2:D:729:ILE:HG :C:685:LYS:HE3 1:C:710:ASN:HB :A:242:GLY:O 1:A:243:SER:C :A:220:ILE:HA 1:A:248::HB :A:534:LYS:O 1:A:757:GLY:HA :C:839:ARG:CZ 2:B:582::O :C:531:LYS:HZ2 1:C:777::CD :D:533:ILE:O 2:D:756:PHE:CB :C:432:LYS:HD3 1:C:464:ILE:HD :B:483:GLY:HA3 2:B:494:ASN:HB :C:777::HB3 2:B:516:GLU:CB :A:685:LYS:HE3 1:A:710:ASN:HB :D:534:SER:HB2 2:D:750:ILE:HG :A:26:ILE:CD1 1:A:58:ILE:HG :A:28:ASN:ND2 1:A:85:SER:O :A:558:PHE:HA 2:B:814:ILE:HG :D:558:VAL:CG1 1:A:813:MET:HE :A:432:LYS:HD3 1:A:464:ILE:HD :A:531:LYS:HB2 1:A:776:ILE:HD :D:483:GLY:HA3 2:D:494:ASN:HB :D:780::H 1:A:521:ASN:ND :C:521:ASN:HD22 2:B:780::C :C:697:VAL:O 2:D:431:ARG:NH :D:434:VAL:O 2:D:456:CYS:HB :B:533:ILE:CG2 2:B:729:ILE:HG :B:665::O 2:B:671:GLN:NE :C:519:ILE:HG23 1:C:529:PHE:CD :A:242:GLY:O 1:A:243:SER:O :B:538:SER:CA 2:B:748:VAL:H

26 Page 26 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1:C:242:GLY:O 1:C:243:SER:C :C:531:LYS:HB2 1:C:776:ILE:HD :D:535:VAL:HA 2:D:729:ILE:HA :D:636:PHE:CB 1:A:615::HD :A:124:ARG:NH1 1:A:251:GLU:OE :D:759:THR:OG1 1:A:780:HIS:ND :C:125:MET:SD 1:C:252:ARG:NH :D:220:LYS:HZ2 2:B:220:LYS:HG :D:510:GLY:O 2:D:528:PHE:CE :A:152:PHE:O 1:A:155:MET:HB :B:434:VAL:O 2:B:456:CYS:HB :C:817:PHE:CG 2:B:561:MET:HE :A:697:VAL:O 2:B:431:ARG:NH :B:510:GLY:O 2:B:528:PHE:CE :A:125:MET:SD 1:A:252:ARG:NH :C:366:ILE:HB 1:C:373:ILE:HB :D:738:LYS:HA 2:D:741:ARG:HB :D:538:SER:CA 2:D:748:VAL:H :A:234::C 1:A:237:MET:HB :D:643::CB 1:A:651::CD :C:242:GLY:O 1:C:243:SER:O :C:519:ILE:CG2 1:C:529:PHE:CE :A:519:ILE:HG23 1:A:529:PHE:HE :A:519:ILE:CG2 1:A:529:PHE:CE :A:73:GLN:HG2 2:B:321:TYR:HD :B:682:PHE:CD1 2:B:727::O :C:124:ARG:NH1 1:C:251:GLU:OE :C:152:PHE:O 1:C:155:MET:HB :D:216:GLN:HA 2:D:219::HB :C:55:SER:N 1:C:293:HIS:CE :C:615::HD22 2:B:636:PHE:CB :D:35:ASN:HA 2:D:68:ASN:O :D:535:VAL:HA 2:D:729:ILE:CA :D:791::HD23 2:D:794::HD :B:216:GLN:HA 2:B:219::HB :C:55:SER:O 1:C:293:HIS:HE :A:352:SER:HA 1:A:365:GLY:O :A:355:ASN:HB2 1:A:362:VAL:HB :D:777::O 1:A:521:ASN:CG :C:372:VAL:HG12 1:C:374::HD :D:741:ARG:NH2 2:D:795:TRP:O

27 Page 27 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1:A:146:HIS:NE2 1:A:345:ASP:OD :A:372:VAL:HG12 1:A:374::HD :B:738:LYS:HA 2:B:741:ARG:HB :C:26:ILE:CD1 1:C:58:ILE:HG :C:608:TRP:CD2 2:B:629:ILE:CD :C:537:GLY:H 1:C:752::HD :A:537:GLY:H 1:A:752::HD :B:536:MET:O 2:B:727::C :C:234::C 1:C:237:MET:HB :C:73:GLN:HG2 2:D:321:TYR:HD :B:791::HD23 2:B:794::HD :C:146:HIS:NE2 1:C:345:ASP:OD :D:561:MET:HE2 1:A:817:PHE:CG :D:582::O 1:A:839:ARG:CZ :A:335:THR:OG1 1:A:346:ARG:NH :A:366:ILE:HB 1:A:373:ILE:HB :A:519:ILE:HG23 1:A:529:PHE:CD :B:35:ASN:HA 2:B:68:ASN:O :B:515:ASN:HB2 2:B:518:ARG:H :C:817:PHE:CE1 2:B:561:MET:HE :C:352:SER:HA 1:C:365:GLY:O :A:193:LYS:NZ 1:A:210:GLU:O :B:175:THR:HG22 2:B:206::HB :C:335:THR:OG1 1:C:346:ARG:NH :C:531:LYS:NZ 1:C:777::CD :D:516:GLU:CB 1:A:777::CD :A:531:LYS:NZ 1:A:777::CD :D:645:TYR:CZ 1:A:810:PHE:HE :D:220:LYS:HG3 2:B:220:LYS:HZ :B:536:MET:HB3 2:B:728:PHE:HB :B:741:ARG:NH2 2:B:795:TRP:O :B:537:VAL:HG23 2:B:748:VAL:CB :A:519:ILE:HG12 1:A:529:PHE:CG :C:839:ARG:HH22 2:B:582::HG :D:175:THR:HG22 2:D:206::HB :A:488:GLU:HB2 1:A:499:ASN:HD :A:26:ILE:CD1 1:A:58:ILE:HG :A:775:SER:C 1:A:777::N :C:488:GLU:HB2 1:C:499:ASN:HD :D:515:ASN:HB2 2:D:518:ARG:H :D:740:GLY:HA2 2:D:800:CYS:H

28 Page 28 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 1:A:55:SER:N 1:A:293:HIS:CE :C:648:THR:CG2 2:B:643::CB :B:720::HB3 2:B:747::HD :C:682::HB1 1:C:710:ASN:HA :D:35:ASN:O 2:D:97:GLY:N :A:341:ASN:HD22 1:A:345:ASP:HB :A:682::HB1 1:A:710:ASN:HA :B:291:ARG:HG2 2:B:360:ARG:HH :C:519:ILE:HG12 1:C:529:PHE:CG :A:55:SER:O 1:A:293:HIS:HE :B:35:ASN:O 2:B:97:GLY:N :C:341:ASN:HD22 1:C:345:ASP:HB :C:751:GLU:HB3 1:C:755:ARG:HH :A:160:TRP:HZ3 1:A:391:GLY:H :D:582::HG2 1:A:839:ARG:HH :C:839:ARG:CZ 2:B:582::CG :C:193:LYS:NZ 1:C:210:GLU:O :C:521:ASN:CG 2:B:777::O :D:291:ARG:HG2 2:D:360:ARG:HH :D:162:MET:HE1 2:D:228::HD :A:751:GLU:HB3 1:A:755:ARG:HH :C:160:TRP:HZ3 1:C:391:GLY:H :D:561:MET:HG3 1:A:817:PHE:CZ :B:361::HB2 2:B:378:TRP:HB :C:355:ASN:HB2 1:C:362:VAL:HB :C:364:VAL:HA 1:C:375:ASN:HB :C:531:LYS:C 1:C:776:ILE:CD :A:317:THR:O 1:A:321:PHE:N :C:820:VAL:HG11 2:B:634:TRP:CD :A:145:SER:O 1:A:148:SER:OG :D:536:MET:HB3 2:D:728:PHE:HB :D:720::HB3 2:D:747::HD :B:162:MET:HE1 2:B:228::HD :B:538:SER:C 2:B:746:LYS:O :B:503:GLN:HA 2:B:766:GLN:HE :A:406:GLU:HG2 1:A:410:TYR:HA :C:536:GLN:HE22 1:C:734::HB :C:79:CYS:HB3 2:D:80:LYS:HE :A:79:CYS:HB3 2:B:80:LYS:HE :B:38:VAL:O 2:B:71::HA :A:155:MET:O 1:A:159:SER:N

29 Page 29 Full wwpdb/emdatabank EM Map/Model Validation Report 6IRH 2:D:780::HB2 1:A:521:ASN:CB :A:494:ASN:HB3 2:B:193:ASN:HB :C:521:ASN:HD21 2:B:780::H :B:740:GLY:HA2 2:B:800:CYS:H :C:494:ASN:HB3 2:D:193:ASN:HB :C:519:ILE:HG23 1:C:529:PHE:HE :C:55:SER:H 1:C:293:HIS:CE :D:503:GLN:HA 2:D:766:GLN:HE :D:38:VAL:O 2:D:71::HA :A:364:VAL:HA 1:A:375:ASN:HB :D:216:GLN:C 2:B:220:LYS:NZ :D:35:ASN:HB3 2:D:95:ILE:HG :D:536:MET:O 2:D:727::CB :A:531:LYS:C 1:A:776:ILE:CD :A:610:SER:O 1:A:614::HB :D:216:GLN:C 2:B:220:LYS:HZ :C:610:SER:O 1:C:614::HB :D:538:SER:C 2:D:746:LYS:O :C:406:GLU:HG2 1:C:410:TYR:HA :D:572:ILE:CD1 1:A:828:ILE:HD :C:813:MET:HE2 2:B:558:VAL:CG :D:437:ARG:HD3 2:D:451:ASN:HB :D:780::C 1:A:521:ASN:HD :B:535:VAL:N 2:B:729:ILE:HG :C:138::HD22 1:C:344:GLY:HA :C:531:LYS:HZ3 1:C:777::CD :B:437:ARG:HD3 2:B:451:ASN:HB :C:780:HIS:ND1 2:B:759:THR:OG :D:361::HB2 2:D:378:TRP:HB :A:138::HD22 1:A:344:GLY:HA :A:531:LYS:NZ 1:A:777::CD :A:56:TRP:CB 1:A:59:GLN:HB :D:220:LYS:NZ 2:B:220:LYS:HG :D:538:SER:C 2:D:748:VAL:CG :A:58:ILE:O 1:A:58:ILE:HG :B:694:ILE:O 2:B:698:TYR:N :B:526:VAL:HG22 2:B:779::CD :C:775:SER:C 1:C:777::N :D:123::HG3 2:D:334::HD :D:157:VAL:HG21 2:D:361::HD :D:220:LYS:HZ1 2:B:216:GLN:C