Full wwpdb/emdatabank EM Map/Model Validation Report i

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1 Full wwpdb/emdatabank EM Map/Model Validation Report i Feb 17, :08 pm GMT PDB ID : 5IZ7 EMDB ID: : EMD-8139 Title : Cryo-EM structure of thermally stable Zika virus strain H/PF/2013 Authors : Kostyuchenko, V.A.; Zhang, S.; Fibriansah, G.; Lok, S.M. Deposited on : Resolution : 3.70 Å(reported) Based on PDB ID : 3J27 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 Mogul : (157068), CSD as539be (2018) 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) : trunk30686

2 Page 2 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 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 3.70 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 B C D 75 2 E 75 2 F 75

3 Page 3 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 2 Entry composition i There are 3 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 structural protein E. Mol Chain Residues Atoms AltConf Trace 1 A 504 Total C N O S C 504 Total C N O S B 504 Total C N O S Molecule 2 is a protein called structural protein M. Mol Chain Residues Atoms AltConf Trace 2 D 75 Total C N O S E 75 Total C N O S F 75 Total C N O S Molecule 3 is N-ACETYL-D-GLUCOSAMINE (three-letter code: NAG) (formula: C 8 H 15 NO 6 ).

4 Page 4 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 Mol Chain Residues Atoms AltConf 3 A 1 Total C N O C 1 Total C N O B 1 Total C N O

5 Page 5 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 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: structural protein E Chain A: G435 G436 A437 L438 N439 S440 L441 G442 K443 G444 I445 H446 Q447 I448 F449 F453 K454 S455 L456 F457 G458 G459 M460 S461 W462 F463 S464 Q465 I466 L467 I468 G469 T470 L471 L472 M473 W474 L475 G476 L477 N478 T479 K480 N481 I484 L489 G492 G493 V494 L495 I496 F497 L498 S499 A504 K373 M374 M375 L376 E377 L378 D379 P380 P381 F382 G383 D384 S385 Y386 I387 V388 I389 G390 V391 G392 E393 K394 K395 I396 T397 H398 H399 W400 H401 R402 S405 T406 I407 G408 K409 A410 F411 E412 V415 R416 G417 A418 K419 R420 M421 A422 V423 L424 G425 D426 T427 A428 W429 D430 F431 G432 S433 V434 T313 F314 T315 K316 I317 P318 A319 E320 T321 L322 H323 G324 T325 V326 T327 V328 E329 V330 Q331 Y332 A333 G334 T335 D336 G337 P338 C339 K340 V341 P342 A343 Q344 M345 A346 V347 D348 M349 Q350 T351 L352 T353 P354 V355 G356 R357 L358 I359 T360 A361 N362 P363 V364 I365 T366 E367 S368 T369 E370 N371 S372 K251 R252 Q253 T254 V255 V256 V257 L258 G259 S260 Q261 E262 G263 A264 V265 H266 T267 A268 L269 A270 G271 A272 L273 E274 A275 E276 M277 K281 G282 R283 L284 S285 S286 G287 H288 L289 K290 C291 R292 L293 K294 M295 D296 K297 L298 R299 L300 K301 G302 Y305 S306 L307 C308 T309 A310 A311 F312 G187 L188 D189 C190 E191 P192 R193 T194 G195 L196 D197 F198 S199 D200 L201 Y202 Y203 L204 T205 K209 H210 W211 L212 V213 H214 K215 E216 W217 F218 H219 D220 I221 P222 L223 P224 W225 H226 A227 G228 A229 D230 T231 G232 T233 P234 H235 W236 N237 N238 K239 E240 A241 L242 V243 E244 F245 K246 D247 A248 T126 G127 K128 S129 I130 Q131 P132 E133 N134 L135 E136 Y137 R138 I139 M140 L141 S142 V143 H144 G145 S146 Q147 H148 S149 G150 M151 I152 V153 N154 D155 T156 G157 H158 E159 T160 D161 E162 N163 R164 A165 K166 V167 E168 I169 T170 P171 N172 S173 P174 R175 A176 E177 A178 T179 L180 G181 G182 F183 L186 Y61 E62 A63 S64 I65 S66 D67 M68 A69 S70 D71 S72 R73 C74 P75 T76 Q77 G78 E79 A80 Y81 L82 D83 K84 Q85 S86 D87 T88 Q89 Y90 V91 C92 K93 R94 T95 L96 V97 D98 R99 G100 W101 G106 L107 F108 G109 K110 G111 S112 L113 V114 T115 K118 F119 A120 K123 K124 M125 I1 R2 C3 I4 G5 V6 S7 N8 R9 D10 F11 V12 E13 G14 M15 S16 G17 G18 T19 W20 V21 D22 V23 V24 L25 E26 H27 G28 G29 C30 V31 T32 V33 M34 A35 Q36 D37 K38 P39 T40 V41 D42 I43 E44 L45 V46 T47 T48 T49 V50 S51 N52 M53 A54 E55 V56 R57 S58 Y59 C60 Molecule 1: structural protein E Chain C: G127 K128 S129 I130 Q131 P132 E133 N134 L135 E136 Y137 R138 I139 M140 L141 S142 V143 H144 G145 S146 Q147 H148 S149 G150 M151 I152 V153 N154 D155 H158 D161 E162 N163 R164 V167 E168 I169 T170 P171 N172 R175 A176 E177 A178 T179 L180 G181 G182 F183 G184 S185 L186 G187 L188 D189 C190 S64 I65 S66 D67 M68 A69 S70 D71 S72 R73 C74 P75 T76 Q77 G78 E79 A80 Y81 L82 D83 K84 Q85 S86 D87 T88 Q89 Y90 V91 C92 K93 R94 T95 L96 V97 D98 R99 G100 W101 G102 L107 F108 G109 K110 G111 S112 L113 V114 T115 C116 A117 K118 F119 A120 C121 S122 K123 K124 M125 T126 I1 R2 C3 I4 G5 V6 R9 D10 F11 V12 E13 G14 M15 T19 W20 V21 D22 V23 V24 L25 E26 H27 G28 G29 C30 V31 T32 V33 M34 A35 Q36 D37 K38 P39 T40 V41 D42 I43 E44 L45 V46 T47 T48 T49 V50 S51 N52 M53 A54 E55 V56 R57 S58 Y59 C60 Y61 E62 A63

6 Page 6 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 E191 P192 R193 T194 G195 L196 D200 L201 Y202 Y203 L204 T205 M206 N207 N208 K209 H210 W211 L212 V213 H214 K215 E216 W217 F218 H219 D220 I221 P222 L223 P224 W225 H226 D230 T233 P234 H235 W236 N237 N238 K239 E240 A241 L242 V243 E244 F245 K246 D247 A248 H249 A250 K251 R252 Q253 T254 V255 V256 V257 L258 G259 S260 Q261 E262 G263 A264 V265 H266 T267 A268 L269 A272 L273 E274 A275 E276 M277 K281 G282 R283 L284 S285 S286 G287 H288 L289 K290 C291 R292 L293 K294 M295 D296 K297 L298 R299 L300 K301 G302 V303 S304 Y305 S306 L307 C308 T309 A310 A311 F312 T313 F314 T315 K316 I317 P318 A319 E320 T321 L322 H323 G324 T325 V326 T327 V328 E329 V330 Q331 Y332 A333 G334 T335 D336 G337 P338 C339 K340 V341 P342 A343 Q344 M345 A346 V347 D348 M349 Q350 T351 L352 T353 P354 V355 G356 R357 L358 I359 T360 A361 N362 I365 T366 E367 S368 T369 E370 N371 S372 K373 M374 M375 L376 E377 L378 D379 P380 P381 F382 G383 D384 S385 Y386 I387 V388 I389 G390 V391 G392 E393 K394 K395 I396 T397 H398 H399 W400 H401 R402 I407 G408 K409 R416 G417 A418 K419 R420 M421 A422 V423 L424 G425 D426 T427 A428 W429 D430 F431 G432 S433 V434 G435 G436 A437 L438 N439 S440 L441 G442 K443 G444 I445 H446 Q447 I448 F453 K454 S455 L456 F457 G458 G459 M460 S461 W462 F463 S464 Q465 I466 L467 I468 G469 T470 L471 L472 M473 W474 L475 G476 L477 S485 C488 L489 A490 L491 V494 L495 I496 F497 L498 S499 T500 A501 V502 S503 A504 Molecule 1: structural protein E Chain B: I1 R2 C3 I4 G5 V6 S7 N8 R9 D10 F11 V12 E13 G14 M15 S16 G17 G18 T19 W20 V21 D22 V23 V24 L25 E26 H27 G28 G29 C30 V31 T32 V33 Q36 D37 K38 P39 T40 V41 D42 I43 E44 L45 V46 T47 T48 T49 V50 S51 N52 M53 A54 E55 V56 R57 S58 Y59 C60 Y61 E62 A63 S64 I65 S66 D71 S72 R73 C74 P75 T76 Q77 G78 E79 A80 Y81 L82 D83 K84 Q85 S86 D87 T88 Q89 Y90 V91 C92 K93 R94 T95 L96 V97 D98 R99 G100 W101 G102 N103 G104 C105 G106 L107 F108 G109 K110 G111 S112 L113 V114 A117 K118 S122 K123 K124 G127 K128 S129 I130 Q131 P132 E133 N134 L135 E136 Y137 R138 I139 M140 L141 S142 V143 H144 Q147 H148 S149 G150 M151 I152 V153 N154 D155 T156 G157 H158 E159 T160 D161 E162 N163 R164 A165 K166 V167 E168 I169 T170 P171 N172 S173 P174 R175 A176 L180 G181 G182 F183 G184 S185 L186 G187 L188 D189 C190 E191 P192 R193 T194 G195 L196 D197 F198 S199 D200 L201 Y202 Y203 L204 T205 M206 N207 N208 K209 H210 W211 L212 V213 H214 K215 E216 W217 F218 I221 P222 L223 P224 W225 H226 A227 G228 A229 D230 T231 G232 T233 P234 H235 W236 N237 N238 K239 E240 A241 L242 V243 E244 F245 K246 D247 A248 H249 A250 K251 R252 Q253 T254 V255 V256 V257 L258 G259 S260 Q261 E262 G263 A264 V265 H266 T267 A268 L269 A270 G271 A272 A275 E276 M277 D278 G279 A280 K281 G282 R283 L284 S285 S286 G287 H288 L289 K290 C291 R292 L293 K294 M295 D296 K297 L298 R299 L300 K301 G302 V303 S304 Y305 S306 L307 C308 T309 A310 A311 F312 T313 F314 T315 K316 I317 P318 A319 E320 T321 L322 H323 G324 T325 V326 T327 V328 E329 V330 Q331 Y332 A333 G334 T335 D336 G337 P338 C339 K340 V341 P342 A343 Q344 M345 M349 Q350 T351 L352 T353 P354 V355 G356 R357 L358 I359 T360 A361 N362 P363 V364 I365 T366 E367 S368 T369 E370 N371 S372 K373 M374 M375 L376 E377 L378 D379 P380 P381 F382 G383 D384 S385 Y386 I387 V388 I389 G390 V391 G392 E393 K394 K395 I396 T397 H398 H399 W400 H401 G404 I407 G408 K409 A413 T414 V415 R416 G417 A418 K419 R420 M421 A422 V423 L424 G425 D426 T427 A428 W429 D430 F431 G432 S433 V434 G435 G436 A437 L438 N439 S440 L441 G442 K443 G444 I445 H446 Q447 I448 F449 G450 A451 A452 F453 K454 S455 L456 F457 G458 G459 M460 S461 W462 F463 S464 Q465 L471 L472 M473 W474 L475 G476 L477 N478 T479 K480 N481 G482 S483 I484 S485 L486 M487 C488 L489 A490 L491 G492 G493 V494 L495 I496 F497 L498 S499 A504 Molecule 2: structural protein M Chain D: A1 V2 T3 L4 P5 S6 H7 S8 T9 R10 K11 L12 Q13 T14 R15 S16 Q17 T18 W19 L20 E21 S22 R23 E24 Y25 T26 K27 H28 L29 I30 R31 V32 E33 N34 W35 I36 F37 R38 N39 P40 G41 F42 A43 L44 A45 A46 A47 A48 I49 A50 W51 L52 L53 G54 S55 S56 Q59 K60 V61 I62 Y63 L64 V65 M66 I67 L68 L69 I70 A71 P72 A73 Y74 S75

7 Page 7 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 Molecule 2: structural protein M Chain E: L64 V65 M66 I67 L68 L69 I70 A71 P72 A73 Y74 S75 A1 V2 T3 L4 P5 S6 H7 S8 T9 R10 K11 L12 Q13 T14 R15 S16 Q17 T18 W19 L20 E21 S22 R23 E24 Y25 T26 K27 H28 L29 I30 R31 V32 E33 N34 W35 I36 F37 R38 N39 P40 G41 F42 A46 I49 A50 W51 L52 L53 G54 S55 S56 T57 S58 Q59 K60 V61 I62 Y63 Molecule 2: structural protein M Chain F: I62 Y63 M66 I67 L68 L69 I70 A71 P72 A73 Y74 S75 A1 V2 T3 L4 P5 S6 H7 S8 T9 R10 K11 L12 Q13 T14 R15 S16 Q17 T18 W19 L20 E21 S22 R23 E24 Y25 T26 K27 H28 L29 I30 R31 V32 E33 N34 W35 I36 F37 R38 G41 F42 A43 L44 A45 A46 A47 A48 I49 A50 W51 L52 L53 G54 S55 S56 T57 S58 Q59 K60 V61

8 Page 8 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 4 Experimental information i Property Value Source Reconstruction method SINGLE PARTICLE Depositor Imposed symmetry POINT, I Depositor Number of particles used 7180 Depositor Resolution determination method FSC CUT-OFF Depositor CTF correction method PHASE FLIPPING AND AMPLITUDE Depositor CORRECTION; correction for astigmatism included Microscope FEI TITAN KRIOS Depositor Voltage (kv) 300 Depositor Electron dose (e /Å 2 ) 50 Depositor Minimum defocus (nm) Not provided Depositor Maximum defocus (nm) Not provided Depositor Magnification Not provided Depositor Image detector FEI FALCON II (4k x 4k) Depositor

9 Page 9 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 5 Model quality i 5.1 Standard geometry i Bond lengths and bond angles in the following residue types are not validated in this section: NAG 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 / /5261 (0.1%) 1 B / /5261 (0.2%) 1 C /3887 (0.0%) /5261 (0.2%) 2 D / /838 (0.1%) 2 E / /838 2 F / /838 (0.1%) All All /13508 (0.0%) /18297 (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 2 F 0 1 All (1) bond length outliers are listed below: Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å) 1 C 225 TRP CB-CG All (24) bond angle outliers are listed below: Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 1 C 334 GLY N-CA-C B 224 PRO N-CA-C B 82 LEU N-CA-C C 348 ASP N-CA-C B 456 LEU CA-CB-CG B 438 LEU CA-CB-CG

10 Page 10 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 Mol Chain Res Type Atoms Z Observed( o ) Ideal( o ) 1 B 378 LEU CA-CB-CG C 204 LEU CA-CB-CG C 392 GLY N-CA-C D 5 PRO N-CA-C A 458 GLY N-CA-C A 358 LEU N-CA-C A 310 ALA N-CA-C B 230 ASP N-CA-C A 251 LYS N-CA-C C 3 CYS CA-CB-SG B 308 CYS CA-CB-SG F 54 GLY N-CA-C B 228 GLY N-CA-C C 226 HIS N-CA-C A 309 THR N-CA-C C 348 ASP CB-CG-OD B 27 HIS N-CA-C C 310 ALA N-CA-C There are no chirality outliers. All (1) planarity outliers are listed below: Mol Chain Res Type Group 2 F 74 TYR Sidechain 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 B C D E F A B

11 Page 11 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes 3 C 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 90. All (2386) close contacts within the same asymmetric unit are listed below, sorted by their clash magnitude. 1:C:68:MET:SD 1:C:255:VAL:HB :B:345:MET:HE3 1:B:380:PRO:HA :C:178:ALA:HB3 1:C:186:LEU:H :A:158:HIS:HB3 1:A:166:LYS:HE :B:60:CYS:HB3 1:B:224:PRO:HG :B:271:GLY:HA3 2:E:7:HIS:CD :A:50:VAL:HG11 1:A:130:ILE:HD :A:332:TYR:HB3 1:A:335:THR:HG :E:55:SER:HA 2:E:60:LYS:HG :C:34:MET:HE1 1:C:359:ILE:HG :B:286:SER:HB3 2:E:16:SER:HB :A:73:ARG:NH2 1:A:77:GLN:HB :C:65:ILE:HD11 1:C:243:VAL:HG :E:56:SER:HB3 2:E:59:GLN:HB :B:71:ASP:HB2 1:B:82:LEU:HD :B:95:THR:HG22 1:B:96:LEU:H :C:12:VAL:HG13 1:C:33:VAL:HG :C:93:LYS:HB2 1:C:245:PHE:HE :C:211:TRP:HE1 1:C:269:LEU:HD :B:1:ILE:HG21 1:B:147:GLN:HB :B:41:VAL:HG22 1:B:143:VAL:HG :D:56:SER:HB3 2:D:59:GLN:HG :A:152:ILE:HG12 1:A:153:VAL:H :A:479:THR:HG22 1:A:480:LYS:H :A:332:TYR:HB3 1:A:335:THR:CG :A:263:GLY:O 1:A:267:THR:HG :C:25:LEU:HD23 1:C:43:ILE:HD :B:100:GLY:HA3 1:B:108:PHE:CE :B:21:VAL:HG11 1:B:293:LEU:HB :C:300:LEU:HD23 1:C:301:LYS:H :C:337:GLY:HA2 1:C:368:SER:HA :D:32:VAL:HG23 2:D:72:PRO:HG

12 Page 12 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 2:D:67:ILE:HA 2:D:70:ILE:HG :C:245:PHE:HB3 1:C:255:VAL:HA :B:21:VAL:HG13 1:B:293:LEU:H :D:55:SER:HA 2:D:60:LYS:HE :A:46:VAL:HG12 1:A:47:THR:HG :D:18:THR:HG23 2:D:21:GLU:HB :A:299:ARG:NH1 1:A:299:ARG:HB :B:180:LEU:H 1:B:180:LEU:HD :B:223:LEU:HB2 1:B:224:PRO:HD :A:152:ILE:HG12 1:A:153:VAL:N :B:43:ILE:HG23 1:B:141:LEU:HB :A:359:ILE:HD11 1:A:377:GLU:HG :C:2:ARG:HD2 1:C:44:GLU:OE :B:25:LEU:HD13 1:B:139:ILE:HG :B:221:ILE:HD12 2:E:4:LEU:HA :B:32:THR:HA 1:B:42:ASP:HB :B:57:ARG:HA 1:B:227:ALA:CB :C:59:TYR:O 1:C:124:LYS:HB :C:20:TRP:HA 1:C:293:LEU:O :A:175:ARG:HG2 1:A:189:ASP:HB :B:20:TRP:O 1:B:433:SER:HB :B:4:ILE:H 1:B:151:MET:HE :C:345:MET:HB2 1:C:355:VAL:O :D:23:ARG:HB3 2:D:27:LYS:HE :D:56:SER:CB 2:D:59:GLN:HG :B:137:TYR:HD2 1:B:289:LEU:HD :C:27:HIS:CE1 1:C:48:THR:HG :C:55:GLU:HA 1:C:128:LYS:HA :B:272:ALA:HB2 2:E:18:THR:HG :C:100:GLY:HA3 1:C:108:PHE:CE :A:265:VAL:HG23 2:D:4:LEU:HD :A:37:ASP:O 1:A:300:LEU:HD :E:56:SER:HB3 2:E:59:GLN:CB :A:204:LEU:H 1:A:204:LEU:HD :B:236:TRP:HB2 1:B:239:LYS:HE :C:331:GLN:OE1 1:C:371:ASN:HB :A:1:ILE:HD13 1:A:144:HIS:HA :A:302:GLY:HA3 1:A:305:TYR:CD :B:1:ILE:HG21 1:B:147:GLN:CB :A:150:GLY:C 1:A:152:ILE:H :A:305:TYR:HB2 1:A:340:LYS:HG

13 Page 13 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:A:20:TRP:CE3 1:A:434:VAL:HG :C:65:ILE:HD13 1:C:257:VAL:HG :B:30:CYS:SG 1:B:31:VAL:N :B:95:THR:HG22 1:B:96:LEU:N :B:272:ALA:CB 2:E:18:THR:HG :C:39:PRO:HD2 1:C:298:LEU:HD :C:315:THR:HG21 1:C:373:LYS:HE :C:93:LYS:HB2 1:C:245:PHE:CE :C:389:ILE:HD11 1:C:396:ILE:HG :B:170:THR:HG22 1:B:171:PRO:HD :A:312:PHE:HB3 1:A:396:ILE:HD :A:331:GLN:HG3 1:A:373:LYS:HG :A:38:LYS:HE3 1:A:38:LYS:HA :C:211:TRP:NE1 1:C:269:LEU:HD :C:154:ASN:HB2 3:C:601:NAG:H :B:95:THR:CG2 1:B:96:LEU:H :B:21:VAL:CG1 1:B:293:LEU:HB :A:358:LEU:O 1:A:359:ILE:HG :A:56:VAL:HG23 1:B:78:GLY:HA :D:23:ARG:CB 2:D:27:LYS:HE :C:217:TRP:NE1 2:F:5:PRO:HB :B:48:THR:HG23 1:B:284:LEU:HG :C:300:LEU:HD23 1:C:301:LYS:N :C:13:GLU:HG2 1:C:34:MET:HG :A:47:THR:OG1 1:A:138:ARG:HD :C:65:ILE:HD11 1:C:243:VAL:CG :D:1:ALA:CB 2:F:23:ARG:HD :A:314:PHE:HD1 1:A:314:PHE:H :A:392:GLY:C 1:A:394:LYS:H :A:305:TYR:CB 1:A:340:LYS:HG :B:486:LEU:HD23 1:B:487:MET:H :B:345:MET:HG2 1:B:378:LEU:HD :A:171:PRO:HA 1:A:192:PRO:CG :A:169:ILE:HD11 1:A:289:LEU:HD :C:337:GLY:HA2 1:C:368:SER:CA :B:175:ARG:HA 1:B:188:LEU:O :C:41:VAL:HG23 1:C:143:VAL:HG :B:375:MET:C 1:B:376:LEU:HG :C:420:ARG:HD2 1:C:431:PHE:CD :A:76:THR:HG21 1:A:107:LEU:HD :B:23:VAL:HG21 1:B:31:VAL:HG

14 Page 14 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:A:405:SER:HB2 1:A:408:GLY:HA :E:71:ALA:N 2:E:72:PRO:HD :C:337:GLY:CA 1:C:368:SER:HA :A:171:PRO:HA 1:A:192:PRO:HG :A:65:ILE:HD12 1:A:257:VAL:HG :C:28:GLY:HA3 2:F:15:ARG:HG :B:71:ASP:O 1:B:113:LEU:HB :A:352:LEU:H 1:A:352:LEU:HD :B:269:LEU:O 2:E:19:TRP:HD :C:457:PHE:O 1:C:460:MET:HG :A:302:GLY:HA3 1:A:305:TYR:CE :B:40:THR:HG23 1:B:144:HIS:HD :C:133:GLU:O 1:C:134:ASN:HB :D:1:ALA:N 2:F:27:LYS:HD :C:154:ASN:CB 3:C:601:NAG:H :A:2:ARG:HB2 1:A:142:SER:CB :A:460:MET:HG3 1:A:464:SER:HB :B:320:GLU:HB2 1:B:400:TRP:HZ :A:97:VAL:O 1:A:110:LYS:HG :F:4:LEU:HD23 2:F:5:PRO:HD :B:486:LEU:HD23 1:B:487:MET:N :C:389:ILE:HD11 1:C:396:ILE:CG :A:493:GLY:HA2 1:A:496:ILE:HD :A:341:VAL:HG22 1:A:365:ILE:HG :D:49:ILE:HA 2:D:52:LEU:HD :B:137:TYR:CD2 1:B:289:LEU:HD :C:426:ASP:HB3 1:C:446:HIS:CB :A:115:THR:HG22 1:A:253:GLN:NE :A:332:TYR:CB 1:A:335:THR:HG :B:60:CYS:H 1:B:224:PRO:HD :B:66:SER:OG 1:B:118:LYS:HB :C:439:ASN:C 1:C:441:LEU:H :F:27:LYS:HG3 2:F:28:HIS:H :C:273:LEU:N 2:F:12:LEU:HD :A:138:ARG:HH21 1:A:140:MET:HE :C:184:GLY:HA3 1:C:297:LYS:O :B:262:GLU:O 1:B:265:VAL:HG :A:46:VAL:HG21 1:A:140:MET:HG :B:97:VAL:HG13 1:B:251:LYS:HA :C:178:ALA:O 1:C:185:SER:HB :D:73:ALA:HB2 2:F:74:TYR:CE

15 Page 15 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:B:151:MET:O 1:B:153:VAL:HG :A:312:PHE:HD2 1:A:396:ILE:HB :B:21:VAL:HG13 1:B:293:LEU:N :A:261:GLN:CA 1:A:261:GLN:HE :B:21:VAL:HG11 1:B:293:LEU:CB :C:429:TRP:HB3 1:C:442:GLY:O :B:57:ARG:HA 1:B:227:ALA:HB :B:33:VAL:HG22 1:B:41:VAL:O :C:475:LEU:HD13 2:D:52:LEU:HD :A:20:TRP:HE3 1:A:434:VAL:HG :B:313:THR:HA 1:B:396:ILE:HD :C:238:ASN:HA 1:C:240:GLU:OE :B:25:LEU:CD1 1:B:139:ILE:HG :C:115:THR:HG21 1:C:253:GLN:HB :B:1:ILE:HD11 1:B:142:SER:OG :C:137:TYR:CD2 1:C:289:LEU:HD :C:34:MET:CE 1:C:359:ILE:HG :C:419:LYS:HB3 2:F:15:ARG:HH :A:65:ILE:HB 1:A:257:VAL:HG :B:99:ARG:HH21 1:B:103:ASN:HB :B:396:ILE:HG12 1:B:396:ILE:O :C:210:HIS:CD2 1:C:277:MET:H :A:118:LYS:HG2 1:A:119:PHE:H :B:223:LEU:CB 1:B:224:PRO:HD :A:332:TYR:HD2 1:A:335:THR:HB :B:107:LEU:H 1:B:107:LEU:HD :B:107:LEU:N 1:B:107:LEU:HD :B:260:SER:O 1:B:261:GLN:HB :B:73:ARG:HB3 1:B:77:GLN:HE :A:252:ARG:HB2 1:A:252:ARG:NH :B:181:GLY:C 1:B:183:PHE:H :B:434:VAL:HG13 1:B:436:GLY:H :B:382:PHE:HB3 1:B:404:GLY:O :A:50:VAL:HG11 1:A:130:ILE:CD :C:97:VAL:O 1:C:99:ARG:HD :B:49:THR:HG22 1:B:283:ARG:HG :A:43:ILE:HG23 1:A:141:LEU:HD :A:314:PHE:CE2 1:A:318:PRO:HD :A:305:TYR:HE1 1:A:338:PRO:HG :B:137:TYR:CE2 1:B:289:LEU:HD :B:40:THR:HG23 1:B:144:HIS:CD

16 Page 16 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:B:12:VAL:CG1 1:B:33:VAL:HG :C:68:MET:SD 1:C:255:VAL:CB :A:240:GLU:HA 1:A:243:VAL:HG :B:481:ASN:ND2 1:B:483:SER:HB :A:1:ILE:O 1:A:4:ILE:HG :F:27:LYS:HG3 2:F:28:HIS:N :C:462:TRP:CZ3 1:C:499:SER:HB :B:365:ILE:HG22 1:B:366:THR:O :C:137:TYR:HE2 1:C:289:LEU:HB :C:273:LEU:HD21 1:C:286:SER:HB :C:344:GLN:HE21 1:C:354:PRO:HB :D:10:ARG:HH21 2:D:10:ARG:HG :D:11:LYS:HD2 2:D:18:THR:HG :E:62:ILE:O 2:E:65:VAL:HG :B:204:LEU:O 1:B:210:HIS:HB :A:2:ARG:HB2 1:A:142:SER:HB :C:491:LEU:O 1:C:495:LEU:HG :A:322:LEU:HG 1:A:323:HIS:H :B:27:HIS:CD2 1:B:45:LEU:HD :D:31:ARG:HG2 2:F:4:LEU:HB :D:50:ALA:HB1 2:D:60:LYS:HB :A:2:ARG:HG2 1:A:44:GLU:OE :B:198:PHE:HA 1:B:201:LEU:HB :B:485:SER:HA 1:B:488:CYS:SG :C:171:PRO:HB2 1:C:193:ARG:HD :C:98:ASP:OD1 1:C:110:LYS:HG :A:344:GLN:O 1:A:388:VAL:HG :A:373:LYS:O 1:A:374:MET:HB :C:423:VAL:HG22 1:C:502:VAL:HG :C:178:ALA:HB3 1:C:186:LEU:N :B:171:PRO:HA 1:B:192:PRO:HB :A:139:ILE:HB 1:A:167:VAL:HG :B:175:ARG:HB2 1:B:175:ARG:CZ :C:89:GLN:HA 1:C:239:LYS:NZ :C:34:MET:HE1 1:C:359:ILE:CG :B:158:HIS:HB3 1:B:164:ARG:HD :B:12:VAL:HG11 1:B:33:VAL:HG :C:422:ALA:HB1 1:C:498:LEU:CD :A:12:VAL:HG11 1:A:432:GLY:HA :C:9:ARG:HH11 1:C:32:THR:HG :D:67:ILE:HA 2:D:70:ILE:CG

17 Page 17 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 2:E:66:MET:O 2:E:70:ILE:HG :B:133:GLU:O 1:B:134:ASN:HB :B:357:ARG:HB2 1:B:357:ARG:HH :B:223:LEU:HB2 1:B:224:PRO:CD :C:423:VAL:CG2 1:C:502:VAL:HG :B:4:ILE:HA 1:B:9:ARG:HE :A:360:THR:CG2 1:A:377:GLU:H :B:27:HIS:CE1 1:B:285:SER:HA :D:67:ILE:HD12 2:D:70:ILE:HG :A:356:GLY:O 1:A:357:ARG:HB :A:336:ASP:HA 1:A:368:SER:O :A:154:ASN:HB2 3:A:601:NAG:H :B:261:GLN:HE21 2:E:1:ALA:N :B:386:TYR:O 1:B:388:VAL:HG :C:15:MET:SD 1:C:36:GLN:HB :C:74:CYS:HB3 1:C:75:PRO:HD :A:307:LEU:N 1:A:307:LEU:HD :A:409:LYS:HB3 1:A:409:LYS:NZ :A:95:THR:HG23 1:A:96:LEU:HD :C:300:LEU:HD22 1:C:303:VAL:HG :D:35:TRP:HE3 2:D:36:ILE:HD :B:360:THR:OG1 1:B:376:LEU:HB :C:273:LEU:H 2:F:12:LEU:HD :D:41:GLY:C 2:D:43:ALA:H :B:32:THR:CA 1:B:42:ASP:HB :B:19:THR:HB 1:B:295:MET:HB :C:24:VAL:HG11 1:C:424:LEU:HD :C:426:ASP:HB3 1:C:446:HIS:HB :C:475:LEU:HD11 2:D:52:LEU:HB :A:51:SER:OG 1:A:281:LYS:HE :A:65:ILE:HB 1:A:257:VAL:CG :C:164:ARG:HH11 1:C:164:ARG:HG :B:138:ARG:HB2 1:B:138:ARG:NH :B:269:LEU:O 2:E:19:TRP:CD :C:167:VAL:HG22 1:C:168:GLU:H :D:9:THR:HG22 2:D:10:ARG:N :B:38:LYS:HA 1:B:300:LEU:HD :B:38:LYS:HG2 1:B:39:PRO:CD :B:426:ASP:C 1:B:428:ALA:H :D:12:LEU:HD12 2:D:12:LEU:H :B:320:GLU:HB2 1:B:400:TRP:CZ

18 Page 18 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:B:138:ARG:HB2 1:B:138:ARG:HH :B:222:PRO:O 1:B:223:LEU:HG :A:46:VAL:CG1 1:A:47:THR:HG :C:50:VAL:HG11 1:C:130:ILE:HG :E:51:TRP:HD1 2:E:60:LYS:HZ :C:1:ILE:H1 1:C:1:ILE:HD :C:329:GLU:HG3 1:C:375:MET:HB :C:374:MET:C 1:C:375:MET:HE :D:53:LEU:HD13 2:F:62:ILE:HG :A:443:LYS:NZ 1:A:443:LYS:HB :B:154:ASN:HB2 1:B:158:HIS:CE :B:323:HIS:CD2 1:B:416:ARG:HH :B:74:CYS:O 1:B:76:THR:N :B:365:ILE:HA 1:B:374:MET:SD :C:143:VAL:HB 1:C:163:ASN:ND :A:347:VAL:HG23 1:A:355:VAL:HB :A:448:ILE:HG13 1:A:449:PHE:HD :C:139:ILE:HB 1:C:167:VAL:CG :C:374:MET:O 1:C:374:MET:SD :C:223:LEU:HD22 1:C:242:LEU:HD :A:203:TYR:HE2 1:A:277:MET:CE :B:330:VAL:O 1:B:373:LYS:HA :A:476:GLY:HA3 1:A:489:LEU:HG :B:1:ILE:HD12 1:B:2:ARG:N :B:393:GLU:HG3 1:B:394:LYS:H :B:74:CYS:SG 1:B:99:ARG:HB :A:154:ASN:CB 3:A:601:NAG:H :B:373:LYS:O 1:B:373:LYS:HG :B:41:VAL:HG22 1:B:143:VAL:CG :D:44:LEU:O 2:D:48:ALA:HB :A:131:GLN:O 1:A:133:GLU:N :B:238:ASN:O 1:B:239:LYS:HB :D:49:ILE:HD11 2:D:67:ILE:HG :A:174:PRO:O 1:A:189:ASP:HA :C:307:LEU:HG 1:C:340:LYS:HD :B:271:GLY:CA 2:E:7:HIS:CD :C:139:ILE:HB 1:C:167:VAL:HG :C:344:GLN:NE2 1:C:354:PRO:HB :B:479:THR:HG21 1:B:485:SER:CB :A:154:ASN:CG 3:A:601:NAG:H :A:479:THR:HG22 1:A:480:LYS:N

19 Page 19 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:B:21:VAL:HG22 1:B:21:VAL:O :B:60:CYS:CB 1:B:224:PRO:HG :C:97:VAL:HG21 1:C:113:LEU:HD :C:39:PRO:HG2 1:C:183:PHE:HE :A:169:ILE:HD12 1:A:190:CYS:HB :B:141:LEU:CD1 1:B:165:ALA:HB :B:73:ARG:CB 1:B:77:GLN:HE :C:50:VAL:HG11 1:C:130:ILE:CG :C:39:PRO:HG2 1:C:183:PHE:CE :C:26:GLU:HB3 1:C:288:HIS:HA :A:73:ARG:HG3 1:A:79:GLU:O :B:212:LEU:HD12 1:B:275:ALA:HB :B:82:LEU:O 1:B:82:LEU:HG :A:307:LEU:HD22 1:A:307:LEU:H :A:360:THR:HG21 1:A:377:GLU:H :C:273:LEU:HD12 1:C:274:GLU:N :C:276:GLU:OE1 1:C:276:GLU:N :F:32:VAL:O 2:F:36:ILE:HG :A:204:LEU:H 1:A:204:LEU:CD :B:57:ARG:NH1 1:B:225:TRP:NE :B:261:GLN:NE2 2:E:1:ALA:N :C:137:TYR:CE2 1:C:289:LEU:HB :A:44:GLU:HG3 1:A:46:VAL:HG :B:246:LYS:O 1:B:254:THR:HG :B:27:HIS:HD2 1:B:45:LEU:HD :B:345:MET:HE3 1:B:380:PRO:CA :B:38:LYS:HG2 1:B:39:PRO:HD :B:141:LEU:HD11 1:B:165:ALA:HB :C:114:VAL:O 1:C:114:VAL:HG :C:133:GLU:HB2 1:C:193:ARG:HH :A:314:PHE:HE2 1:A:318:PRO:HD :A:290:LYS:HD2 1:A:427:THR:HG :A:397:THR:O 1:A:397:THR:HG :B:225:TRP:CZ3 1:B:226:HIS:HA :B:445:ILE:HG23 1:B:446:HIS:H :A:329:GLU:HB2 1:C:101:TRP:CZ :A:305:TYR:CE1 1:A:338:PRO:HG :A:461:SER:OG 2:D:8:SER:HB :B:227:ALA:C 1:B:229:ALA:N :C:326:VAL:HG21 1:C:380:PRO:HG :E:51:TRP:HD1 2:E:60:LYS:NZ

20 Page 20 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:A:455:SER:O 2:F:41:GLY:HA :B:494:VAL:O 1:B:498:LEU:HG :C:41:VAL:HG23 1:C:143:VAL:CG :C:422:ALA:HB1 1:C:498:LEU:HD :B:297:LYS:O 1:B:298:LEU:HG :A:23:VAL:HG13 1:A:25:LEU:HD :A:39:PRO:HD3 1:A:300:LEU:HD :C:347:VAL:O 1:C:348:ASP:HB :A:141:LEU:HB2 1:A:165:ALA:HB :A:31:VAL:HB 1:A:43:ILE:HD :B:268:ALA:HA 2:E:4:LEU:HD :B:197:ASP:C 1:B:199:SER:H :C:332:TYR:O 1:C:371:ASN:HA :A:1:ILE:HG23 1:A:152:ILE:HG :C:312:PHE:O 1:C:396:ILE:HG :A:252:ARG:HB2 1:A:252:ARG:CZ :A:312:PHE:CG 1:A:389:ILE:HB :B:186:LEU:HD23 1:B:293:LEU:HD :B:113:LEU:HD22 1:B:114:VAL:N :B:40:THR:CG2 1:B:144:HIS:HD :A:157:GLY:C 1:A:159:GLU:H :C:196:LEU:HD13 1:C:288:HIS:HB :B:442:GLY:HA2 1:B:445:ILE:HG :C:170:THR:HB 1:C:171:PRO:HD :C:300:LEU:HD22 1:C:303:VAL:CG :C:445:ILE:HD13 1:C:448:ILE:HD :F:56:SER:HB3 2:F:59:GLN:HB :A:43:ILE:HG23 1:A:141:LEU:CD :A:342:PRO:HG2 1:A:389:ILE:HG :C:36:GLN:O 1:C:38:LYS:N :A:300:LEU:N 1:A:300:LEU:HD :C:70:SER:HB2 1:C:115:THR:HA :C:389:ILE:O 1:C:389:ILE:HD :C:460:MET:HE2 1:C:468:ILE:HD :B:359:ILE:HB 1:B:377:GLU:HB :C:319:ALA:O 1:C:326:VAL:HG :C:327:THR:HB 1:C:329:GLU:OE :A:130:ILE:HG21 1:A:198:PHE:HD :A:7:SER:O 1:A:8:ASN:HB :B:222:PRO:C 1:B:223:LEU:HD :A:135:LEU:N 1:A:135:LEU:HD

21 Page 21 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:B:73:ARG:HG3 1:B:79:GLU:O :C:100:GLY:HA3 1:C:108:PHE:CD :D:55:SER:CA 2:D:60:LYS:HE :B:38:LYS:HG3 1:B:298:LEU:CB :D:1:ALA:H2 2:F:27:LYS:HD :F:9:THR:HG22 2:F:10:ARG:NH :A:28:GLY:HA3 2:D:15:ARG:HG :C:204:LEU:O 1:C:210:HIS:HB :D:71:ALA:HB3 2:D:72:PRO:CD :B:53:MET:HB2 1:B:128:LYS:HD :C:467:LEU:HD13 2:F:69:LEU:HD :A:158:HIS:CB 1:A:166:LYS:HE :A:144:HIS:ND1 1:A:360:THR:HG :A:85:GLN:HE22 1:A:94:ARG:HH :B:261:GLN:NE2 2:E:1:ALA:H :B:23:VAL:CG2 1:B:31:VAL:HG :C:92:CYS:HB3 1:C:115:THR:O :C:284:LEU:HD22 1:C:285:SER:O :A:25:LEU:O 1:A:45:LEU:HB :C:320:GLU:OE2 1:C:402:ARG:HG :A:261:GLN:HA 1:A:261:GLN:HE :A:377:GLU:O 1:A:378:LEU:HB :C:347:VAL:HG13 1:C:347:VAL:O :C:384:ASP:O 1:C:385:SER:HB :C:460:MET:CE 1:C:468:ILE:HD :B:12:VAL:HG13 1:B:12:VAL:O :B:31:VAL:O 1:B:43:ILE:HD :B:91:VAL:HG13 1:B:91:VAL:O :C:184:GLY:HA3 1:C:297:LYS:C :C:295:MET:CE 1:C:298:LEU:HB :C:426:ASP:HB3 1:C:446:HIS:HB :E:6:SER:HB2 2:E:8:SER:HB :D:1:ALA:HB2 2:F:23:ARG:HD :B:57:ARG:NH1 1:B:225:TRP:HE :B:305:TYR:HB3 1:B:339:CYS:HA :B:377:GLU:O 1:B:378:LEU:HD :D:29:LEU:O 2:D:29:LEU:HD :E:28:HIS:O 2:E:32:VAL:HG :A:118:LYS:HG2 1:A:119:PHE:N :A:307:LEU:CD2 1:A:307:LEU:H :E:4:LEU:C 2:E:4:LEU:HD

22 Page 22 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 2:F:71:ALA:HB3 2:F:72:PRO:HD :B:357:ARG:NH1 1:B:357:ARG:HB :B:316:LYS:HB2 1:B:329:GLU:HB :A:150:GLY:HA2 1:A:152:ILE:HG :A:299:ARG:HB2 1:A:299:ARG:CZ :B:38:LYS:HG3 1:B:298:LEU:HB :B:432:GLY:HA3 1:B:439:ASN:HD :B:261:GLN:HE21 2:E:1:ALA:H :B:6:VAL:C 1:B:8:ASN:H :A:295:MET:HA 1:A:295:MET:HE :A:27:HIS:CD2 1:A:285:SER:HA :B:138:ARG:O 1:B:138:ARG:HG :C:171:PRO:HA 1:C:192:PRO:HB :A:150:GLY:C 1:A:152:ILE:N :A:204:LEU:N 1:A:204:LEU:HD :A:65:ILE:CG2 1:A:66:SER:N :B:187:GLY:O 1:B:293:LEU:HA :C:39:PRO:HD2 1:C:298:LEU:CD :C:329:GLU:HB3 1:C:373:LYS:NZ :C:300:LEU:HD11 1:C:362:ASN:HB :B:197:ASP:O 1:B:199:SER:N :B:309:THR:HA 1:B:391:VAL:HG :C:475:LEU:CD1 2:D:52:LEU:HD :E:52:LEU:O 2:E:53:LEU:HD :B:357:ARG:HD3 1:B:359:ILE:HD :C:329:GLU:HB3 1:C:373:LYS:HZ :A:360:THR:HG21 1:A:376:LEU:HA :C:315:THR:CG2 1:C:373:LYS:HE :A:34:MET:HB3 1:A:40:THR:HG :B:286:SER:HB3 2:E:16:SER:CB :E:46:ALA:O 2:E:49:ILE:HG :A:151:MET:O 1:A:151:MET:HG :A:169:ILE:HG13 1:A:169:ILE:O :C:273:LEU:HB2 2:F:12:LEU:CD :D:3:THR:OG1 2:F:31:ARG:HD :A:299:ARG:HH11 1:A:299:ARG:HB :A:341:VAL:HG22 1:A:365:ILE:CG :B:3:CYS:O 1:B:9:ARG:NE :A:175:ARG:HG2 1:A:189:ASP:CB :B:138:ARG:CB 1:B:138:ARG:HH :B:6:VAL:O 1:B:8:ASN:N

23 Page 23 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:A:6:VAL:HG12 1:A:9:ARG:HB :B:7:SER:H 1:B:322:LEU:HD :C:454:LYS:O 1:C:458:GLY:HA :D:21:GLU:HG3 2:D:22:SER:N :A:56:VAL:HG11 1:A:202:TYR:CE :B:58:SER:HB3 1:B:226:HIS:O :A:311:ALA:CB 1:A:334:GLY:H :A:343:ALA:O 1:A:344:GLN:HB :A:477:LEU:HD23 1:A:477:LEU:O :A:191:GLU:HG3 1:A:290:LYS:HB :B:38:LYS:HA 1:B:300:LEU:CD :B:99:ARG:HH21 1:B:103:ASN:CB :B:214:HIS:H 2:E:7:HIS:CE :C:148:HIS:O 1:C:152:ILE:HG :B:12:VAL:HG12 1:B:33:VAL:HA :D:67:ILE:CA 2:D:70:ILE:HG :A:154:ASN:OD1 1:A:156:THR:HG :B:43:ILE:H 1:B:43:ILE:HD :C:135:LEU:O 1:C:171:PRO:HD :A:360:THR:HG23 1:A:377:GLU:HB :B:37:ASP:C 1:B:300:LEU:HD :B:343:ALA:CB 1:B:389:ILE:HG :B:471:LEU:O 1:B:475:LEU:HG :C:283:ARG:CZ 1:C:283:ARG:HB :D:29:LEU:O 2:D:32:VAL:HG :D:55:SER:HA 2:D:60:LYS:CE :B:57:ARG:NH1 1:B:225:TRP:CD :C:12:VAL:CG1 1:C:33:VAL:HG :D:2:VAL:O 2:D:2:VAL:HG :B:187:GLY:O 1:B:188:LEU:HD :C:12:VAL:O 1:C:12:VAL:HG :A:18:GLY:O 1:A:19:THR:OG :A:300:LEU:N 1:A:300:LEU:CD :A:387:ILE:O 1:A:388:VAL:HG :B:343:ALA:HB1 1:B:389:ILE:HG :B:221:ILE:CD1 2:E:4:LEU:HA :A:59:TYR:CE2 1:A:221:ILE:HB :E:24:GLU:O 2:E:27:LYS:HG :B:313:THR:H 1:B:330:VAL:HG :C:441:LEU:O 1:C:444:GLY:N :B:100:GLY:CA 1:B:108:PHE:CE

24 Page 24 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:B:225:TRP:CE3 1:B:226:HIS:N :B:32:THR:HA 1:B:42:ASP:CB :A:138:ARG:HH21 1:A:140:MET:CE :A:158:HIS:HB3 1:A:166:LYS:CE :B:93:LYS:HB3 1:B:245:PHE:CD :C:141:LEU:O 1:C:164:ARG:HA :A:261:GLN:NE2 1:C:263:GLY:HA :C:240:GLU:OE2 1:C:241:ALA:N :B:56:VAL:HG11 1:B:202:TYR:CD :A:302:GLY:HA3 1:A:305:TYR:HD :A:454:LYS:NZ 1:A:454:LYS:HB :A:345:MET:O 1:A:354:PRO:HA :A:73:ARG:CZ 1:A:77:GLN:HB :B:91:VAL:HG11 1:B:243:VAL:HG :C:97:VAL:HG21 1:C:113:LEU:CD :C:65:ILE:H 1:C:257:VAL:CG :B:58:SER:OG 1:B:124:LYS:HD :B:277:MET:HG3 1:B:279:GLY:N :B:284:LEU:HD12 1:B:285:SER:O :C:161:ASP:HB3 1:C:164:ARG:O :C:345:MET:CB 1:C:355:VAL:O :A:27:HIS:HD2 1:A:285:SER:HA :B:75:PRO:HB3 1:B:110:LYS:HB :C:1:ILE:HD12 1:C:147:GLN:OE :C:37:ASP:O 1:C:300:LEU:HB :F:9:THR:HG22 2:F:10:ARG:HH :A:143:VAL:HG12 1:A:144:HIS:H :B:181:GLY:C 1:B:183:PHE:N :C:375:MET:SD 1:C:375:MET:N :A:426:ASP:C 1:A:428:ALA:H :B:187:GLY:H 1:B:293:LEU:HD :C:426:ASP:CB 1:C:446:HIS:HB :B:54:ALA:HB3 1:B:129:SER:HB :C:144:HIS:O 1:C:145:GLY:C :C:245:PHE:HA 1:C:254:THR:O :A:56:VAL:HG23 1:B:78:GLY:CA :B:180:LEU:N 1:B:180:LEU:HD :B:189:ASP:HB2 1:B:292:ARG:HB :B:225:TRP:CE3 1:B:226:HIS:HA :A:73:ARG:HH21 1:A:77:GLN:HB :B:186:LEU:HD23 1:B:298:LEU:HD

25 Page 25 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:A:459:GLY:HA2 2:D:9:THR:HG :B:56:VAL:HG22 1:B:57:ARG:HG :C:138:ARG:CZ 1:C:138:ARG:HB :C:1:ILE:HD12 1:C:1:ILE:N :B:180:LEU:HD11 1:B:186:LEU:HD :B:283:ARG:HB3 1:B:283:ARG:CZ :C:392:GLY:O 1:C:395:LYS:HE :A:169:ILE:CD1 1:A:190:CYS:HB :A:178:ALA:HB1 1:A:180:LEU:HD :A:226:HIS:CG 1:A:234:PRO:HB :C:295:MET:HE1 1:C:298:LEU:HB :C:70:SER:OG 1:C:253:GLN:NE :B:445:ILE:HG23 1:B:446:HIS:N :C:89:GLN:HA 1:C:239:LYS:HZ :A:1:ILE:HG22 1:A:2:ARG:N :A:493:GLY:O 1:A:496:ILE:HB :B:20:TRP:CE3 1:B:292:ARG:NH :C:295:MET:HE1 1:C:298:LEU:HD :A:359:ILE:CD1 1:A:377:GLU:HG :B:38:LYS:CA 1:B:300:LEU:HD :B:65:ILE:HD12 1:B:65:ILE:O :A:333:ALA:O 1:A:370:GLU:HA :A:472:LEU:HD23 1:A:492:GLY:HA :C:47:THR:HG23 1:C:283:ARG:HD :A:348:ASP:HB2 1:A:350:GLN:CG :B:158:HIS:CB 1:B:164:ARG:HD :B:187:GLY:N 1:B:293:LEU:HD :B:56:VAL:HG11 1:B:202:TYR:HD :B:393:GLU:HG3 1:B:394:LYS:N :C:26:GLU:CB 1:C:288:HIS:HA :A:266:HIS:O 2:D:20:LEU:HD :B:281:LYS:NZ 1:B:281:LYS:HB :B:137:TYR:CD2 1:B:289:LEU:HD :B:479:THR:HG21 1:B:485:SER:OG :B:74:CYS:HB3 1:B:75:PRO:HD :A:203:TYR:HE2 1:A:277:MET:HE :B:159:GLU:HA 1:B:164:ARG:O :F:4:LEU:HD23 2:F:5:PRO:CD :A:97:VAL:HG11 1:A:113:LEU:HD :A:43:ILE:CG2 1:A:141:LEU:HD :B:306:SER:O 1:B:339:CYS:HB

26 Page 26 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 2:F:47:ALA:O 2:F:51:TRP:HB :F:56:SER:HB3 2:F:59:GLN:CG :B:141:LEU:HD12 1:B:165:ALA:O :B:180:LEU:HD11 1:B:186:LEU:CD :F:3:THR:C 2:F:5:PRO:HD :C:84:LYS:O 1:C:86:SER:N :A:58:SER:OG 1:A:126:THR:HG :A:305:TYR:HB3 1:A:340:LYS:HG :A:365:ILE:HG22 1:A:368:SER:HB :B:491:LEU:HA 1:B:494:VAL:HG :C:260:SER:OG 1:C:261:GLN:N :C:427:THR:O 1:C:427:THR:HG :A:265:VAL:CG2 2:D:4:LEU:HD :A:156:THR:O 1:A:158:HIS:N :A:251:LYS:HE2 1:A:252:ARG:HE :D:30:ILE:HG13 2:D:31:ARG:N :A:27:HIS:NE2 1:A:48:THR:HG :B:338:PRO:HD3 1:B:367:GLU:HG :B:74:CYS:CB 1:B:75:PRO:HD :C:185:SER:O 1:C:297:LYS:HB :C:73:ARG:HG2 1:C:79:GLU:N :E:70:ILE:C 2:E:72:PRO:HD :F:67:ILE:C 2:F:69:LEU:H :A:63:ALA:HB1 1:A:119:PHE:HE :B:474:TRP:HZ2 2:E:58:SER:HB :C:334:GLY:CA 1:C:370:GLU:HA :A:96:LEU:H 1:A:96:LEU:HD :B:186:LEU:CD2 1:B:293:LEU:HD :B:56:VAL:O 1:B:227:ALA:HB :C:39:PRO:CG 1:C:300:LEU:HA :A:225:TRP:NE1 1:A:237:ASN:ND :B:345:MET:HG2 1:B:378:LEU:CD :C:298:LEU:HD13 1:C:298:LEU:C :F:51:TRP:HA 2:F:60:LYS:HD :A:86:SER:OG 1:B:235:HIS:HB :C:240:GLU:HA 1:C:243:VAL:HB :C:357:ARG:HG2 1:C:358:LEU:N :B:154:ASN:HB2 1:B:158:HIS:HE :B:258:LEU:HD23 1:B:259:GLY:H :B:472:LEU:HD23 1:B:475:LEU:HD :E:65:VAL:HG22 2:E:69:LEU:CD

27 Page 27 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:C:27:HIS:HE1 1:C:48:THR:HG :A:83:ASP:N 1:A:83:ASP:OD :B:309:THR:HA 1:B:391:VAL:CG :A:38:LYS:HE2 1:A:298:LEU:O :A:312:PHE:CD1 1:A:389:ILE:HB :B:429:TRP:HE1 1:B:446:HIS:HD :C:167:VAL:HG13 1:C:168:GLU:N :C:36:GLN:O 1:C:38:LYS:HG :C:63:ALA:HB2 1:C:242:LEU:HD :C:70:SER:CB 1:C:115:THR:HA :A:45:LEU:HD12 1:A:138:ARG:O :B:135:LEU:HD12 1:B:135:LEU:C :B:349:MET:SD 1:B:349:MET:N :D:23:ARG:CA 2:D:27:LYS:HE :D:71:ALA:HB3 2:D:72:PRO:HD :A:456:LEU:HD13 1:A:457:PHE:CD :C:90:TYR:H 1:C:90:TYR:HD :D:1:ALA:H1 2:F:27:LYS:HD :A:215:LYS:NZ 1:A:215:LYS:HB :A:248:ALA:HB1 1:A:252:ARG:NH :B:360:THR:O 1:B:361:ALA:HB :F:27:LYS:O 2:F:29:LEU:N :A:162:GLU:HG3 1:A:181:GLY:O :B:41:VAL:CG2 1:B:143:VAL:HG :B:20:TRP:HE3 1:B:292:ARG:HH :B:19:THR:CB 1:B:295:MET:H :C:439:ASN:C 1:C:441:LEU:N :D:60:LYS:HD3 2:D:60:LYS:N :B:344:GLN:OE1 1:B:352:LEU:HG :C:445:ILE:HA 1:C:448:ILE:HD :C:90:TYR:N 1:C:90:TYR:CD :A:157:GLY:C 1:A:159:GLU:N :B:225:TRP:C 1:B:225:TRP:CE :A:115:THR:HG21 1:A:253:GLN:O :A:330:VAL:HG22 1:A:374:MET:HG :B:110:LYS:O 1:B:111:GLY:O :B:162:GLU:OE1 1:B:162:GLU:HA :B:489:LEU:O 1:B:489:LEU:HD :F:56:SER:O 2:F:60:LYS:HG :A:9:ARG:HA 1:A:30:CYS:O :B:127:GLY:HA3 1:B:218:PHE:CZ

28 Page 28 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:B:216:GLU:HA 1:B:216:GLU:OE :C:180:LEU:HD23 1:C:184:GLY:O :F:19:TRP:CG 2:F:20:LEU:N :B:71:ASP:OD2 1:B:80:ALA:HB :C:40:THR:O 1:C:143:VAL:HG :C:305:TYR:HB3 1:C:339:CYS:HA :D:56:SER:HB3 2:D:59:GLN:CG :D:60:LYS:H 2:D:60:LYS:HD :D:69:LEU:HD23 2:D:69:LEU:O :D:69:LEU:HD22 2:F:70:ILE:HD :B:32:THR:CB 1:B:42:ASP:HB :C:2:ARG:HH12 1:C:155:ASP:CG :C:63:ALA:HB2 1:C:242:LEU:CD :A:423:VAL:C 1:A:425:GLY:H :B:420:ARG:HB3 1:B:420:ARG:NH :A:101:TRP:HZ2 1:C:316:LYS:HB :A:497:PHE:C 1:A:499:SER:H :B:169:ILE:N 1:B:169:ILE:HD :B:302:GLY:O 1:B:304:SER:N :B:479:THR:HG21 1:B:485:SER:HB :A:321:THR:OG1 1:A:325:THR:OG :A:355:VAL:O 1:A:355:VAL:HG :B:101:TRP:CD1 1:B:108:PHE:CE :B:36:GLN:O 1:B:300:LEU:HD :B:417:GLY:O 1:B:421:MET:HB :C:213:VAL:HG11 1:C:217:TRP:CE :C:34:MET:CE 1:C:359:ILE:HD :C:93:LYS:O 1:C:114:VAL:HA :D:21:GLU:O 2:D:23:ARG:N :A:294:LYS:HB3 1:A:296:ASP:OD :C:330:VAL:HG23 1:C:374:MET:CE :A:290:LYS:HE3 1:A:292:ARG:HH :A:392:GLY:C 1:A:394:LYS:N :B:415:VAL:HG12 1:B:419:LYS:HE :B:487:MET:HA 1:B:490:ALA:HB :A:475:LEU:CD1 2:F:53:LEU:HB :A:150:GLY:O 1:A:152:ILE:N :B:227:ALA:C 1:B:229:ALA:H :E:54:GLY:O 2:E:56:SER:N :A:72:SER:HB2 1:A:99:ARG:HH :B:139:ILE:HD13 1:B:167:VAL:HG

29 Page 29 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:C:70:SER:CB 1:C:253:GLN:HE :C:56:VAL:HG12 1:C:127:GLY:O :B:426:ASP:C 1:B:428:ALA:N :C:211:TRP:HE1 1:C:269:LEU:CD :C:21:VAL:HA 1:C:433:SER:HB :C:1:ILE:HG21 1:C:4:ILE:HG :A:2:ARG:HB2 1:A:142:SER:HB :B:1:ILE:HD12 1:B:2:ARG:H :E:42:PHE:O 2:E:46:ALA:CB :A:291:CYS:C 1:A:292:ARG:HD :A:356:GLY:O 1:A:357:ARG:CB :A:3:CYS:O 1:A:9:ARG:HD :B:137:TYR:HB2 1:B:169:ILE:CD :B:201:LEU:HD12 1:B:212:LEU:HB :D:12:LEU:CD1 2:D:12:LEU:H :B:238:ASN:O 1:B:239:LYS:CB :B:93:LYS:HB3 1:B:245:PHE:CE :C:179:THR:C 1:C:180:LEU:HD :D:12:LEU:HD12 2:D:12:LEU:N :F:50:ALA:HB2 2:F:67:ILE:HD :A:115:THR:HG22 1:A:253:GLN:HE :B:130:ILE:O 1:B:130:ILE:HG :B:261:GLN:HA 1:B:261:GLN:OE :B:409:LYS:NZ 1:B:413:ALA:HB :B:73:ARG:HD2 1:B:77:GLN:HG :B:82:LEU:O 1:B:84:LYS:N :C:273:LEU:HB2 2:F:12:LEU:HD :A:49:THR:HG23 1:A:136:GLU:HG :A:348:ASP:HB2 1:A:350:GLN:HG :B:127:GLY:HA2 1:B:204:LEU:HD :C:178:ALA:O 1:C:185:SER:CB :A:1:ILE:N 1:A:144:HIS:NE :A:199:SER:O 1:A:200:ASP:HB :A:34:MET:N 1:A:34:MET:SD :B:137:TYR:HB2 1:B:169:ILE:HD :B:185:SER:O 1:B:186:LEU:HG :B:190:CYS:C 1:B:192:PRO:HD :B:45:LEU:HA 1:B:139:ILE:CG :C:308:CYS:HB3 1:C:332:TYR:HE :A:331:GLN:HG2 1:A:372:SER:O :A:423:VAL:O 1:A:424:LEU:HB

30 Page 30 Full wwpdb/emdatabank EM Map/Model Validation Report 5IZ7 1:B:265:VAL:O 1:B:269:LEU:HB :B:60:CYS:HB3 1:B:224:PRO:CG :C:164:ARG:NH1 1:C:164:ARG:HG :F:7:HIS:C 2:F:9:THR:H :A:341:VAL:HG21 1:A:374:MET:HE :B:415:VAL:HA 1:B:418:ALA:CB :C:113:LEU:HD11 1:C:253:GLN:NE :C:277:MET:HA 1:C:282:GLY:HA :C:338:PRO:HA 1:C:365:ILE:O :C:409:LYS:NZ 1:C:409:LYS:HA :C:428:ALA:O 1:C:430:ASP:N :D:9:THR:HG22 2:D:10:ARG:HG :A:324:GLY:CA 1:A:402:ARG:HH :B:95:THR:O 1:B:112:SER:HA :B:225:TRP:CE3 1:B:226:HIS:CA :B:341:VAL:HG23 1:B:363:PRO:HB :C:90:TYR:CZ 1:C:118:LYS:HG :A:135:LEU:HD23 1:A:135:LEU:H :C:471:LEU:HD23 2:F:62:ILE:HD :A:470:THR:C 1:A:472:LEU:H :A:48:THR:HG23 1:A:284:LEU:HG :A:235:HIS:HD2 1:B:86:SER:HA :C:47:THR:HB 1:C:138:ARG:HB :B:45:LEU:HA 1:B:139:ILE:HG :B:137:TYR:HE2 1:B:289:LEU:HD :B:366:THR:O 1:B:368:SER:N :C:131:GLN:O 1:C:133:GLU:O :C:330:VAL:HG23 1:C:374:MET:HE :C:286:SER:HB3 2:F:16:SER:HB :A:143:VAL:HG11 1:A:183:PHE:CD :A:338:PRO:HA 1:A:365:ILE:O :A:376:LEU:HD12 1:A:376:LEU:O :B:341:VAL:CG2 1:B:363:PRO:HB :A:228:GLY:HA3 1:B:73:ARG:HH :B:181:GLY:O 1:B:183:PHE:N :B:382:PHE:N 1:B:382:PHE:CD :A:382:PHE:CD2 1:A:406:THR:HA :B:216:GLU:O 1:B:218:PHE:N :B:75:PRO:HB3 1:B:110:LYS:CB :C:329:GLU:CG 1:C:375:MET:HB :C:461:SER:O 1:C:464:SER:OG