full wwpdb em validation report i · 2021. 1. 18. · full wwpdb em validation report ......

Full wwPDB EM Validation Report i○

Apr 17, 2021 – 06:20 PM JST

PDB ID : 7DD2EMDB ID : EMD-30642

Title : S-3C1-F2 structure, two RBDs are up and one RBD is down, the two up RBDbind with a 3C1 fab.

Authors : Cong, Y.; Liu, C.X.Deposited on : 2020-10-27

Resolution : 5.60 Å(reported)

This is a Full wwPDB EM Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected] user guide is available at

https://www.wwpdb.org/validation/2017/EMValidationReportHelpwith specific help available everywhere you see the i○ symbol.

The following versions of software and data (see references i○) were used in the production of this report:

EMDB validation analysis : 0.0.0.dev75MolProbity : 4.02b-467

Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Ideal geometry (proteins) : Engh & Huber (2001)

Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.18

https://www.wwpdb.org/validation/2017/EMValidationReportHelp



https://www.wwpdb.org/validation/2017/EMValidationReportHelp#references

Full wwPDB EM Validation Report EMD-30642, 7DD2

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 5.60 Å.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

Metric Whole archive(#Entries)

EM structures(#Entries)

Clashscore 158937 4297Ramachandran outliers 154571 4023

Sidechain outliers 154315 3826

The table below summarises the geometric issues observed across the polymeric chains and their fitto the map. The red, orange, yellow and green segments of the bar indicate the fraction of residuesthat contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A greysegment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions <=5%The upper red bar (where present) indicates the fraction of residues that have poor fit to the EMmap (all-atom inclusion < 40%). The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 C 1261

1 D 1261

1 K 1261

2 A 222

2 E 222

3 B 214

3 H 214

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#overall_quality


2 Entry composition i○

There are 3 unique types of molecules in this entry. The entry contains 31623 atoms, of which 0are hydrogens and 0 are deuteriums.

In the tables below, the AltConf column contains the number of residues with at least one atomin alternate conformation and the Trace column contains the number of residues modelled with atmost 2 atoms.

• Molecule 1 is a protein called Spike glycoprotein.

Mol Chain Residues Atoms AltConf Trace

1 C 1061 Total C N O S8304 5296 1388 1582 38 0 0

1 D 1059 Total C N O S8289 5287 1385 1579 38 0 0

1 K 1061 Total C N O S8304 5296 1388 1582 38 0 0

There are 174 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceC 682 GLY ARG engineered mutation UNP P0DTC2C 683 SER ARG engineered mutation UNP P0DTC2C 685 SER ARG engineered mutation UNP P0DTC2C 986 PRO LYS engineered mutation UNP P0DTC2C 987 PRO VAL engineered mutation UNP P0DTC2C 1209 GLY - expression tag UNP P0DTC2C 1210 SER - expression tag UNP P0DTC2C 1211 GLY - expression tag UNP P0DTC2C 1212 TYR - expression tag UNP P0DTC2C 1213 ILE - expression tag UNP P0DTC2C 1214 PRO - expression tag UNP P0DTC2C 1215 GLU - expression tag UNP P0DTC2C 1216 ALA - expression tag UNP P0DTC2C 1217 PRO - expression tag UNP P0DTC2C 1218 ARG - expression tag UNP P0DTC2C 1219 ASP - expression tag UNP P0DTC2C 1220 GLY - expression tag UNP P0DTC2C 1221 GLN - expression tag UNP P0DTC2C 1222 ALA - expression tag UNP P0DTC2C 1223 TYR - expression tag UNP P0DTC2C 1224 VAL - expression tag UNP P0DTC2C 1225 ARG - expression tag UNP P0DTC2C 1226 LYS - expression tag UNP P0DTC2C 1227 ASP - expression tag UNP P0DTC2

Continued on next page...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#entry_composition


Continued from previous page...Chain Residue Modelled Actual Comment Reference

C 1228 GLY - expression tag UNP P0DTC2C 1229 GLU - expression tag UNP P0DTC2C 1230 TRP - expression tag UNP P0DTC2C 1231 VAL - expression tag UNP P0DTC2C 1232 LEU - expression tag UNP P0DTC2C 1233 LEU - expression tag UNP P0DTC2C 1234 SER - expression tag UNP P0DTC2C 1235 THR - expression tag UNP P0DTC2C 1236 PHE - expression tag UNP P0DTC2C 1237 LEU - expression tag UNP P0DTC2C 1238 GLU - expression tag UNP P0DTC2C 1239 ASN - expression tag UNP P0DTC2C 1240 LEU - expression tag UNP P0DTC2C 1241 TYR - expression tag UNP P0DTC2C 1242 PHE - expression tag UNP P0DTC2C 1243 GLN - expression tag UNP P0DTC2C 1244 GLY - expression tag UNP P0DTC2C 1245 ASP - expression tag UNP P0DTC2C 1246 TYR - expression tag UNP P0DTC2C 1247 LYS - expression tag UNP P0DTC2C 1248 ASP - expression tag UNP P0DTC2C 1249 ASP - expression tag UNP P0DTC2C 1250 ASP - expression tag UNP P0DTC2C 1251 ASP - expression tag UNP P0DTC2C 1252 LYS - expression tag UNP P0DTC2C 1253 HIS - expression tag UNP P0DTC2C 1254 HIS - expression tag UNP P0DTC2C 1255 HIS - expression tag UNP P0DTC2C 1256 HIS - expression tag UNP P0DTC2C 1257 HIS - expression tag UNP P0DTC2C 1258 HIS - expression tag UNP P0DTC2C 1259 HIS - expression tag UNP P0DTC2C 1260 HIS - expression tag UNP P0DTC2C 1261 HIS - expression tag UNP P0DTC2D 682 GLY ARG engineered mutation UNP P0DTC2D 683 SER ARG engineered mutation UNP P0DTC2D 685 SER ARG engineered mutation UNP P0DTC2D 986 PRO LYS engineered mutation UNP P0DTC2D 987 PRO VAL engineered mutation UNP P0DTC2D 1209 GLY - expression tag UNP P0DTC2D 1210 SER - expression tag UNP P0DTC2D 1211 GLY - expression tag UNP P0DTC2




D 1212 TYR - expression tag UNP P0DTC2D 1213 ILE - expression tag UNP P0DTC2D 1214 PRO - expression tag UNP P0DTC2D 1215 GLU - expression tag UNP P0DTC2D 1216 ALA - expression tag UNP P0DTC2D 1217 PRO - expression tag UNP P0DTC2D 1218 ARG - expression tag UNP P0DTC2D 1219 ASP - expression tag UNP P0DTC2D 1220 GLY - expression tag UNP P0DTC2D 1221 GLN - expression tag UNP P0DTC2D 1222 ALA - expression tag UNP P0DTC2D 1223 TYR - expression tag UNP P0DTC2D 1224 VAL - expression tag UNP P0DTC2D 1225 ARG - expression tag UNP P0DTC2D 1226 LYS - expression tag UNP P0DTC2D 1227 ASP - expression tag UNP P0DTC2D 1228 GLY - expression tag UNP P0DTC2D 1229 GLU - expression tag UNP P0DTC2D 1230 TRP - expression tag UNP P0DTC2D 1231 VAL - expression tag UNP P0DTC2D 1232 LEU - expression tag UNP P0DTC2D 1233 LEU - expression tag UNP P0DTC2D 1234 SER - expression tag UNP P0DTC2D 1235 THR - expression tag UNP P0DTC2D 1236 PHE - expression tag UNP P0DTC2D 1237 LEU - expression tag UNP P0DTC2D 1238 GLU - expression tag UNP P0DTC2D 1239 ASN - expression tag UNP P0DTC2D 1240 LEU - expression tag UNP P0DTC2D 1241 TYR - expression tag UNP P0DTC2D 1242 PHE - expression tag UNP P0DTC2D 1243 GLN - expression tag UNP P0DTC2D 1244 GLY - expression tag UNP P0DTC2D 1245 ASP - expression tag UNP P0DTC2D 1246 TYR - expression tag UNP P0DTC2D 1247 LYS - expression tag UNP P0DTC2D 1248 ASP - expression tag UNP P0DTC2D 1249 ASP - expression tag UNP P0DTC2D 1250 ASP - expression tag UNP P0DTC2D 1251 ASP - expression tag UNP P0DTC2D 1252 LYS - expression tag UNP P0DTC2D 1253 HIS - expression tag UNP P0DTC2




D 1254 HIS - expression tag UNP P0DTC2D 1255 HIS - expression tag UNP P0DTC2D 1256 HIS - expression tag UNP P0DTC2D 1257 HIS - expression tag UNP P0DTC2D 1258 HIS - expression tag UNP P0DTC2D 1259 HIS - expression tag UNP P0DTC2D 1260 HIS - expression tag UNP P0DTC2D 1261 HIS - expression tag UNP P0DTC2K 682 GLY ARG engineered mutation UNP P0DTC2K 683 SER ARG engineered mutation UNP P0DTC2K 685 SER ARG engineered mutation UNP P0DTC2K 986 PRO LYS engineered mutation UNP P0DTC2K 987 PRO VAL engineered mutation UNP P0DTC2K 1209 GLY - expression tag UNP P0DTC2K 1210 SER - expression tag UNP P0DTC2K 1211 GLY - expression tag UNP P0DTC2K 1212 TYR - expression tag UNP P0DTC2K 1213 ILE - expression tag UNP P0DTC2K 1214 PRO - expression tag UNP P0DTC2K 1215 GLU - expression tag UNP P0DTC2K 1216 ALA - expression tag UNP P0DTC2K 1217 PRO - expression tag UNP P0DTC2K 1218 ARG - expression tag UNP P0DTC2K 1219 ASP - expression tag UNP P0DTC2K 1220 GLY - expression tag UNP P0DTC2K 1221 GLN - expression tag UNP P0DTC2K 1222 ALA - expression tag UNP P0DTC2K 1223 TYR - expression tag UNP P0DTC2K 1224 VAL - expression tag UNP P0DTC2K 1225 ARG - expression tag UNP P0DTC2K 1226 LYS - expression tag UNP P0DTC2K 1227 ASP - expression tag UNP P0DTC2K 1228 GLY - expression tag UNP P0DTC2K 1229 GLU - expression tag UNP P0DTC2K 1230 TRP - expression tag UNP P0DTC2K 1231 VAL - expression tag UNP P0DTC2K 1232 LEU - expression tag UNP P0DTC2K 1233 LEU - expression tag UNP P0DTC2K 1234 SER - expression tag UNP P0DTC2K 1235 THR - expression tag UNP P0DTC2K 1236 PHE - expression tag UNP P0DTC2K 1237 LEU - expression tag UNP P0DTC2




K 1238 GLU - expression tag UNP P0DTC2K 1239 ASN - expression tag UNP P0DTC2K 1240 LEU - expression tag UNP P0DTC2K 1241 TYR - expression tag UNP P0DTC2K 1242 PHE - expression tag UNP P0DTC2K 1243 GLN - expression tag UNP P0DTC2K 1244 GLY - expression tag UNP P0DTC2K 1245 ASP - expression tag UNP P0DTC2K 1246 TYR - expression tag UNP P0DTC2K 1247 LYS - expression tag UNP P0DTC2K 1248 ASP - expression tag UNP P0DTC2K 1249 ASP - expression tag UNP P0DTC2K 1250 ASP - expression tag UNP P0DTC2K 1251 ASP - expression tag UNP P0DTC2K 1252 LYS - expression tag UNP P0DTC2K 1253 HIS - expression tag UNP P0DTC2K 1254 HIS - expression tag UNP P0DTC2K 1255 HIS - expression tag UNP P0DTC2K 1256 HIS - expression tag UNP P0DTC2K 1257 HIS - expression tag UNP P0DTC2K 1258 HIS - expression tag UNP P0DTC2K 1259 HIS - expression tag UNP P0DTC2K 1260 HIS - expression tag UNP P0DTC2K 1261 HIS - expression tag UNP P0DTC2

• Molecule 2 is a protein called The heavy chain of 3C1 fab.


2 E 221 Total C N O S1691 1069 273 342 7 0 0

2 A 221 Total C N O S1691 1069 273 342 7 0 0

• Molecule 3 is a protein called The light chain of 3C1 fab.


3 H 213 Total C N O S1672 1041 286 338 7 0 0

3 B 213 Total C N O S1672 1041 286 338 7 0 0


3 Residue-property plots i○

These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. Thefirst graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andatom inclusion in map density. Residues are color-coded according to the number of geometricquality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2and red = 3 or more. A red diamond above a residue indicates a poor fit to the EM map forthis residue (all-atom inclusion < 40%). Stretches of 2 or more consecutive residues without anyoutlier are shown as a green connector. Residues present in the sample, but not in the model, areshown in grey.

• Molecule 1: Spike glycoprotein

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https://www.wwpdb.org/validation/2017/EMValidationReportHelp#residue_plots


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4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, Not providedNumber of particles used 31143 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING AND AMPLITUDE

CORRECTIONDepositor

Microscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å2

) 49.6 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 2.631 DepositorMinimum map value -1.434 DepositorAverage map value 0.007 DepositorMap value standard deviation 0.094 DepositorRecommended contour level 0.9 DepositorMap size (Å) 489.59998, 489.59998, 489.59998 wwPDBMap dimensions 480, 480, 480 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.02, 1.02, 1.02 Depositor

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#experimental_info


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 valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).

Mol Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5

1 C 0.25 0/8494 0.43 0/115541 D 0.25 0/8479 0.43 0/115351 K 0.25 0/8494 0.43 0/115542 A 0.24 0/1739 0.45 0/23812 E 0.24 0/1739 0.45 0/23813 B 0.24 0/1712 0.44 0/23243 H 0.25 0/1712 0.45 0/2324All All 0.25 0/32369 0.43 0/44053

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

There are no planarity outliers.

5.2 Too-close contacts i○

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in the chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashes withinthe asymmetric unit, whereas Symm-Clashes lists symmetry-related clashes.

Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 C 8304 0 8101 68 01 D 8289 0 8081 57 01 K 8304 0 8101 55 02 A 1691 0 1626 15 02 E 1691 0 1626 9 03 B 1672 0 1587 12 03 H 1672 0 1587 18 0All All 31623 0 30709 212 0

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#model_quality

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#standard_geometry

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#close_contacts


The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 3.

All (212) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:C:329:PHE:CD2 1:C:330:PRO:HD2 1.97 0.981:C:329:PHE:CE1 1:C:528:LYS:HG3 2.18 0.781:C:329:PHE:CG 1:C:330:PRO:HD2 2.30 0.672:E:40:PHE:HB2 2:E:44:LYS:HB2 1.84 0.59

1:K:1047:TYR:HB2 1:K:1067:TYR:HB3 1.83 0.592:A:39:LYS:HB3 2:A:92:THR:HB 1.86 0.58

1:C:781:VAL:HG22 1:C:1026:ALA:HB2 1.86 0.571:D:902:MET:SD 1:D:905:ARG:NH1 2.78 0.571:C:189:LEU:HB2 1:C:210:ILE:HG12 1.85 0.571:K:902:MET:SD 1:K:905:ARG:NH1 2.78 0.562:A:40:PHE:HB2 2:A:44:LYS:HB3 1.87 0.561:C:1035:GLY:HA3 1:K:1040:VAL:HG21 1.86 0.561:C:328:ARG:HG3 1:C:533:LEU:HD22 1.86 0.561:C:35:GLY:HA3 1:C:56:LEU:HB3 1.88 0.551:D:150:LYS:HG2 1:D:152:TRP:H 1.71 0.541:C:896:ILE:HG23 1:C:901:GLN:HE21 1.72 0.541:C:326:ILE:HB 1:C:541:PHE:HA 1.90 0.54

1:C:212:LEU:HD21 1:C:217:PRO:HG3 1.90 0.531:C:902:MET:SD 1:C:905:ARG:NH1 2.82 0.533:H:14:SER:HB3 3:H:107:LYS:HB2 1.91 0.53

1:D:1040:VAL:HG21 1:K:1035:GLY:HA3 1.90 0.531:C:475:ALA:HB3 1:C:487:ASN:HB3 1.91 0.521:D:97:LYS:HB3 1:D:186:PHE:HA 1.90 0.52

1:D:781:VAL:HG22 1:D:1026:ALA:HB2 1.90 0.521:K:598:ILE:HB 1:K:609:ALA:HB3 1.91 0.511:K:344:ALA:O 1:K:509:ARG:NH1 2.43 0.511:D:329:PHE:O 1:D:580:GLN:NE2 2.43 0.51

3:B:108:ARG:NH1 3:B:170:ASP:O 2.43 0.511:D:50:SER:OG 1:D:304:LYS:NZ 2.44 0.51

1:C:1089:PHE:HB3 1:D:913:GLN:HE21 1.76 0.511:D:1047:TYR:HB2 1:D:1067:TYR:HB3 1.92 0.511:K:246:ARG:HB2 1:K:259:THR:H 1.76 0.511:D:478:THR:HB 3:H:5:THR:HG21 1.94 0.501:K:780:GLU:O 1:K:784:GLN:NE2 2.44 0.503:B:2:ILE:HG23 3:B:27:GLN:HB2 1.92 0.501:C:394:ASN:HB2 1:C:516:GLU:HB3 1.93 0.501:D:481:ASN:ND2 3:H:7:SER:O 2.44 0.50



Continued from previous page...


Clashoverlap (Å)

1:C:376:THR:HB 1:C:435:ALA:HB3 1.94 0.501:D:34:ARG:NH1 1:D:191:GLU:OE2 2.45 0.501:K:68:ILE:HG22 1:K:262:ALA:HA 1.93 0.501:D:24:LEU:HD22 1:D:78:ARG:HD2 1.92 0.501:D:92:PHE:HB3 1:D:192:PHE:HB2 1.94 0.501:K:134:GLN:HB3 1:K:161:SER:HB3 1.94 0.503:B:128:GLY:HA2 3:B:183:LYS:HD2 1.94 0.503:B:33:VAL:HB 3:B:51:ALA:HB2 1.94 0.49

1:D:486:PHE:HB3 3:H:5:THR:HG23 1.94 0.491:K:39:PRO:HG3 1:K:51:THR:HG21 1.94 0.491:C:24:LEU:HD22 1:C:78:ARG:HD2 1.95 0.493:H:54:ARG:NH1 3:H:58:VAL:O 2.46 0.491:C:388:ASN:HB3 1:C:529:LYS:HE3 1.93 0.491:C:102:ARG:NH1 1:C:154:GLU:OE2 2.45 0.491:C:111:ASP:OD2 1:C:113:LYS:NZ 2.45 0.491:C:551:VAL:HB 1:C:588:THR:HB 1.94 0.491:D:246:ARG:NH1 1:D:257:GLY:O 2.46 0.491:D:1056:ALA:HB2 1:D:1061:VAL:HG23 1.95 0.493:B:24:LYS:NZ 3:B:70:ASP:OD1 2.45 0.492:E:11:LEU:HB2 2:E:153:PRO:HG3 1.95 0.482:E:44:LYS:NZ 3:H:100:GLY:O 2.46 0.48

1:C:134:GLN:HB3 1:C:161:SER:HB2 1.94 0.481:C:917:TYR:HB3 1:K:1129:VAL:HG22 1.94 0.481:D:560:LEU:O 1:D:577:ARG:NH2 2.45 0.481:D:809:PRO:HA 1:D:814:LYS:HG2 1.95 0.483:H:149:LYS:HB2 3:H:193:THR:HB 1.95 0.481:K:246:ARG:NH1 1:K:257:GLY:O 2.46 0.483:H:108:ARG:NH1 3:H:170:ASP:O 2.46 0.481:C:676:THR:HG23 1:C:689:SER:HB3 1.96 0.481:C:319:ARG:NH1 1:C:320:VAL:O 2.47 0.483:H:106:ILE:HB 3:H:166:GLN:HE22 1.79 0.481:D:954:GLN:O 1:D:1011:GLN:NE2 2.46 0.47

1:K:436:TRP:HE1 1:K:509:ARG:HD2 1.79 0.473:B:37:GLN:HB2 3:B:47:LEU:HB2 1.96 0.471:D:869:MET:SD 1:D:869:MET:N 2.88 0.471:D:866:THR:OG1 1:D:869:MET:SD 2.73 0.471:K:966:LEU:O 1:K:1000:ARG:NH2 2.47 0.471:C:41:LYS:HB3 1:K:563:GLN:HA 1.95 0.471:D:44:ARG:HB2 1:D:279:TYR:HD2 1.79 0.471:D:58:PHE:HB2 1:D:293:LEU:HD22 1.96 0.473:H:33:VAL:HB 3:H:51:ALA:HB2 1.97 0.47





Clashoverlap (Å)

2:A:3:GLN:NE2 2:A:110:GLY:O 2.48 0.473:H:66:GLY:HA3 3:H:71:PHE:HA 1.96 0.471:K:644:GLN:NE2 1:K:645:THR:O 2.48 0.471:C:289:VAL:HG11 1:C:300:LYS:HB2 1.97 0.471:D:84:LEU:HG 1:D:267:VAL:HG11 1.97 0.471:K:1032:CYS:SG 1:K:1051:SER:OG 2.71 0.471:D:439:ASN:O 1:D:443:SER:OG 2.33 0.47

1:K:725:GLU:OE2 1:K:1028:LYS:NZ 2.41 0.472:E:156:VAL:HG21 2:E:183:LEU:HD11 1.96 0.461:D:785:VAL:HG12 1:D:787:GLN:H 1.80 0.461:C:193:VAL:HB 1:C:204:TYR:HB2 1.97 0.46

1:C:503:VAL:HG11 2:A:100:HIS:HB2 1.97 0.463:B:2:ILE:H 3:B:97:THR:HG21 1.80 0.46

1:C:97:LYS:HB3 1:C:186:PHE:HA 1.98 0.461:D:666:ILE:HD11 1:D:672:ALA:HB2 1.97 0.463:H:113:PRO:HB3 3:H:139:PHE:HB3 1.97 0.461:C:280:ASN:OD1 1:C:284:THR:N 2.47 0.461:K:756:TYR:HH 1:K:998:THR:HG1 1.61 0.461:K:957:GLN:O 1:K:961:THR:OG1 2.32 0.462:E:179:ASP:OD1 2:E:179:ASP:N 2.46 0.461:K:452:LEU:HD13 1:K:492:LEU:HB3 1.97 0.462:A:150:GLY:HA2 2:A:180:LEU:HD13 1.97 0.461:C:552:LEU:HB3 1:C:585:LEU:HD13 1.98 0.451:C:814:LYS:HZ3 1:C:872:GLN:HG2 1.81 0.451:K:401:VAL:HG22 1:K:509:ARG:HG2 1.99 0.451:K:559:PHE:HB3 1:K:584:ILE:HB 1.98 0.451:C:329:PHE:CG 1:C:330:PRO:CD 2.98 0.453:H:128:GLY:HA2 3:H:183:LYS:HB2 1.98 0.451:K:117:LEU:HD22 1:K:231:ILE:HD13 1.98 0.451:C:99:ASN:ND2 1:C:178:ASP:O 2.46 0.45

1:C:1054:GLN:HB2 1:C:1061:VAL:HB 1.99 0.452:A:107:ASP:HB3 3:B:46:LEU:HB2 1.98 0.451:C:58:PHE:HB2 1:C:293:LEU:HD22 1.99 0.451:K:53:ASP:OD2 1:K:195:LYS:NZ 2.50 0.45

1:K:277:LEU:HD22 1:K:285:ILE:HD13 1.99 0.451:K:403:ARG:HG3 1:K:497:PHE:HE1 1.81 0.451:D:1006:THR:HG23 1:K:1005:GLN:HE22 1.82 0.452:A:148:VAL:HG21 2:A:203:VAL:HG11 1.98 0.451:C:498:GLN:NE2 1:C:500:THR:OG1 2.49 0.451:K:99:ASN:ND2 1:K:178:ASP:O 2.43 0.451:K:108:THR:O 1:K:236:THR:OG1 2.34 0.45





Clashoverlap (Å)

1:D:656:VAL:HG12 1:D:658:ASN:H 1.82 0.452:E:148:VAL:HB 2:E:183:LEU:HB2 1.98 0.451:D:294:ASP:N 1:D:294:ASP:OD1 2.49 0.451:D:326:ILE:HB 1:D:541:PHE:HA 1.99 0.451:C:418:ILE:HA 1:C:422:ASN:HB2 1.98 0.441:C:108:THR:O 1:C:236:THR:OG1 2.35 0.44

2:A:177:GLN:HE21 3:B:160:LEU:HD11 1.81 0.441:C:969:ASN:HB2 1:D:755:GLN:HB3 2.00 0.441:C:1056:ALA:HB2 1:C:1061:VAL:HG23 1.98 0.441:D:364:ASP:HA 1:D:527:PRO:HG3 1.98 0.441:K:565:PHE:HA 1:K:576:VAL:HA 1.99 0.441:K:656:VAL:HG12 1:K:658:ASN:H 1.83 0.441:D:328:ARG:NH2 1:D:580:GLN:OE1 2.50 0.441:D:393:THR:HA 1:D:522:ALA:HA 1.99 0.441:D:1074:ASN:OD1 1:K:895:GLN:NE2 2.50 0.443:H:83:LEU:HD22 3:H:166:GLN:HB3 2.00 0.442:A:156:VAL:HG21 2:A:183:LEU:HD11 1.99 0.441:C:656:VAL:HG12 1:C:658:ASN:H 1.83 0.441:C:798:GLY:O 1:C:920:GLN:NE2 2.50 0.44

1:C:338:PHE:HB3 1:C:368:LEU:HD21 1.99 0.431:K:557:LYS:HB2 1:K:584:ILE:HD13 2.01 0.431:C:908:GLY:O 1:C:1038:LYS:NZ 2.52 0.431:K:93:ALA:HA 1:K:191:GLU:HG2 2.00 0.43

1:C:1005:GLN:HE22 1:K:1006:THR:HG23 1.83 0.431:D:216:LEU:HA 1:D:217:PRO:HD3 1.91 0.431:K:128:ILE:HD13 1:K:229:LEU:HD11 1.99 0.431:K:809:PRO:HA 1:K:814:LYS:HG2 1.99 0.431:C:152:TRP:HB3 1:C:179:LEU:HB2 1.99 0.431:D:396:TYR:HB2 1:D:514:SER:HB2 2.00 0.431:D:877:LEU:HD22 1:D:1034:LEU:HD21 2.01 0.43

2:E:62:SER:O 2:E:66:ARG:NH2 2.46 0.431:C:68:ILE:HG22 1:C:262:ALA:HA 2.00 0.431:C:755:GLN:HB2 1:K:969:ASN:HB2 2.01 0.431:D:1054:GLN:HB2 1:D:1061:VAL:HB 2.00 0.431:K:654:GLU:HB3 1:K:693:ILE:HG22 2.00 0.431:D:456:PHE:H 1:D:491:PRO:HB3 1.84 0.43

1:K:719:THR:HG23 1:K:1070:ALA:HB2 2.01 0.431:D:106:PHE:HD2 1:D:117:LEU:HD23 1.84 0.432:A:29:ILE:HD12 2:A:73:THR:HA 2.00 0.431:D:1051:SER:OG 1:D:1064:HIS:ND1 2.49 0.422:E:43:ASN:ND2 3:H:85:ASP:OD2 2.52 0.42





Clashoverlap (Å)

2:A:179:ASP:OD1 2:A:179:ASP:N 2.53 0.421:K:143:VAL:O 1:K:146:HIS:NE2 2.46 0.422:A:18:LEU:HB3 2:A:82:LEU:H 1.83 0.42

1:D:289:VAL:HG13 1:D:297:SER:HB2 2.01 0.421:K:906:PHE:HB3 1:K:911:VAL:HB 2.02 0.421:C:81:ASN:HB3 1:C:239:GLN:HE21 1.83 0.421:C:330:PRO:O 1:C:331:ASN:HB3 2.19 0.42

1:C:401:VAL:HG22 1:C:509:ARG:HG2 2.01 0.421:D:33:THR:HB 1:D:220:PHE:HD1 1.83 0.422:E:219:ARG:HA 2:E:220:ASP:HA 1.75 0.421:C:380:TYR:OH 1:C:408:ARG:NH1 2.52 0.421:C:738:CYS:SG 1:C:764:ASN:ND2 2.91 0.42

1:D:345:THR:HG22 1:D:346:ARG:HG2 2.02 0.421:C:1031:GLU:HA 1:K:1040:VAL:HB 2.02 0.421:D:35:GLY:HA3 1:D:56:LEU:HB3 2.02 0.421:K:294:ASP:OD1 1:K:294:ASP:N 2.52 0.421:C:957:GLN:O 1:C:961:THR:OG1 2.32 0.42

1:D:867:ASP:OD1 1:D:867:ASP:N 2.53 0.421:K:718:PHE:HA 1:K:1069:PRO:HA 2.02 0.421:C:40:ASP:N 1:C:40:ASP:OD1 2.53 0.411:D:111:ASP:N 1:D:111:ASP:OD1 2.52 0.41

3:H:170:ASP:OD1 3:H:170:ASP:N 2.52 0.411:K:35:GLY:HA3 1:K:56:LEU:HB3 2.02 0.411:D:40:ASP:OD1 1:D:40:ASP:N 2.51 0.411:D:519:HIS:O 1:K:41:LYS:NZ 2.45 0.411:D:924:ALA:O 1:D:928:ASN:ND2 2.52 0.411:C:591:SER:OG 1:C:619:GLU:OE1 2.39 0.411:D:1041:ASP:HB2 1:K:1030:SER:HB3 2.02 0.411:C:280:ASN:HD21 1:C:284:THR:HB 1.85 0.411:C:864:LEU:HA 1:K:667:GLY:HA2 2.03 0.413:H:46:LEU:HD21 3:H:49:TYR:HB3 2.01 0.411:C:98:SER:HB3 1:C:181:GLY:HA2 2.03 0.41

1:K:1084:ASP:OD1 1:K:1084:ASP:N 2.53 0.411:C:567:ARG:HG2 1:C:573:THR:HG22 2.02 0.411:D:596:SER:OG 1:D:613:GLN:NE2 2.53 0.411:K:40:ASP:OD1 1:K:40:ASP:N 2.52 0.411:C:1084:ASP:OD1 1:C:1084:ASP:N 2.54 0.411:D:280:ASN:OD1 1:D:284:THR:N 2.54 0.413:B:170:ASP:OD1 3:B:170:ASP:N 2.54 0.413:B:190:ASN:HA 3:B:211:ARG:HE 1.84 0.411:C:33:THR:HB 1:C:220:PHE:HD1 1.85 0.41





Clashoverlap (Å)

1:C:674:TYR:HE1 1:C:692:ILE:HG12 1.86 0.412:A:219:ARG:HA 2:A:220:ASP:HA 1.72 0.411:K:1010:GLN:O 1:K:1014:ARG:NH1 2.54 0.401:C:531:THR:HB 1:C:532:ASN:H 1.62 0.401:K:557:LYS:NZ 1:K:586:ASP:OD2 2.48 0.403:B:138:ASN:HA 3:B:172:THR:HB 2.03 0.401:C:490:PHE:O 1:C:493:GLN:NE2 2.50 0.403:H:38:GLN:HG2 3:H:44:PRO:HB3 2.03 0.401:D:435:ALA:HB1 1:D:508:TYR:HB3 2.02 0.402:A:114:THR:HB 2:A:155:PRO:HG3 2.03 0.402:A:148:VAL:HB 2:A:183:LEU:HD12 2.04 0.40

There are no symmetry-related clashes.

5.3 Torsion angles i○

5.3.1 Protein backbone i○

In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all PDB entries followed by that with respect to all EMentries.

The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 C 1047/1261 (83%) 1017 (97%) 29 (3%) 1 (0%) 51 85

1 D 1045/1261 (83%) 1024 (98%) 21 (2%) 0 100 100

1 K 1047/1261 (83%) 1017 (97%) 30 (3%) 0 100 100

2 A 219/222 (99%) 214 (98%) 5 (2%) 0 100 100

2 E 219/222 (99%) 217 (99%) 2 (1%) 0 100 100

3 B 211/214 (99%) 206 (98%) 5 (2%) 0 100 100

3 H 211/214 (99%) 207 (98%) 4 (2%) 0 100 100

All All 3999/4655 (86%) 3902 (98%) 96 (2%) 1 (0%) 100 100

All (1) Ramachandran outliers are listed below:

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#torsion_angles

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_backbone


Mol Chain Res Type1 C 331 ASN

5.3.2 Protein sidechains i○

In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all EMentries.

The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 C 928/1099 (84%) 917 (99%) 11 (1%) 71 84

1 D 926/1099 (84%) 918 (99%) 8 (1%) 78 88

1 K 928/1099 (84%) 917 (99%) 11 (1%) 71 84

2 A 197/198 (100%) 192 (98%) 5 (2%) 47 68

2 E 197/198 (100%) 193 (98%) 4 (2%) 55 73

3 B 190/191 (100%) 190 (100%) 0 100 100

3 H 190/191 (100%) 186 (98%) 4 (2%) 53 72

All All 3556/4075 (87%) 3513 (99%) 43 (1%) 72 84

All (43) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 C 33 THR1 C 208 THR1 C 327 VAL1 C 329 PHE1 C 336 CYS1 C 524 VAL1 C 531 THR1 C 534 VAL1 C 599 THR1 C 760 CYS1 C 912 THR1 D 33 THR1 D 150 LYS1 D 208 THR1 D 510 VAL1 D 599 THR1 D 760 CYS


https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_sidechains


Continued from previous page...Mol Chain Res Type1 D 912 THR1 D 961 THR2 E 57 THR2 E 85 VAL2 E 158 VAL2 E 217 VAL3 H 19 VAL3 H 36 TYR3 H 92 ASN3 H 146 VAL1 K 33 THR1 K 90 VAL1 K 208 THR1 K 329 PHE1 K 392 PHE1 K 394 ASN1 K 510 VAL1 K 573 THR1 K 599 THR1 K 912 THR1 K 916 LEU2 A 71 ARG2 A 143 THR2 A 147 LEU2 A 156 VAL2 A 158 VAL

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (21)such sidechains are listed below:

Mol Chain Res Type1 C 239 GLN1 C 334 ASN1 C 422 ASN1 C 564 GLN1 C 901 GLN1 C 1005 GLN1 C 1011 GLN1 D 437 ASN1 D 613 GLN1 D 957 GLN2 E 76 ASN3 H 89 GLN



Continued from previous page...Mol Chain Res Type3 H 124 GLN3 H 166 GLN1 K 613 GLN1 K 955 ASN1 K 965 GLN1 K 1005 GLN1 K 1011 GLN2 A 161 ASN2 A 177 GLN

5.3.3 RNA i○

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains i○

There are no non-standard protein/DNA/RNA residues in this entry.

5.5 Carbohydrates i○

There are no monosaccharides in this entry.

5.6 Ligand geometry i○

There are no ligands in this entry.

5.7 Other polymers i○

There are no such residues in this entry.

5.8 Polymer linkage issues i○

There are no chain breaks in this entry.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#rna

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligands




https://www.wwpdb.org/validation/2017/EMValidationReportHelp#polymer_linkage


6 Map visualisation i○

This section contains visualisations of the EMDB entry EMD-30642. These allow visual inspectionof the internal detail of the map and identification of artifacts.

No raw map or half-maps were deposited for this entry and therefore no images, graphs, etc.pertaining to the raw map can be shown.

6.1 Orthogonal projections i○

6.1.1 Primary map

X Y Z

The images above show the map projected in three orthogonal directions.

6.2 Central slices i○

6.2.1 Primary map

X Index: 240 Y Index: 240 Z Index: 240

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_visualisation

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_projections

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#central_slices


The images above show central slices of the map in three orthogonal directions.

6.3 Largest variance slices i○

6.3.1 Primary map

X Index: 235 Y Index: 232 Z Index: 227

The images above show the largest variance slices of the map in three orthogonal directions.

6.4 Orthogonal surface views i○

6.4.1 Primary map

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.9.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#largest_variance_slices

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_views


6.5 Mask visualisation i○

This section was not generated. No masks/segmentation were deposited.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#masks


7 Map analysis i○

This section contains the results of statistical analysis of the map.

7.1 Map-value distribution i○

The map-value distribution is plotted in 128 intervals along the x-axis. The y-axis is logarithmic.A spike in this graph at zero usually indicates that the volume has been masked.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_analysis

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_value_distribution


7.2 Volume estimate i○

The volume at the recommended contour level is 481 nm3; this corresponds to an approximatemass of 435 kDa.

The volume estimate graph shows how the enclosed volume varies with the contour level. Therecommended contour level is shown as a vertical line and the intersection between the line andthe curve gives the volume of the enclosed surface at the given level.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#volume_estimate


7.3 Rotationally averaged power spectrum i○

*Reported resolution corresponds to spatial frequency of 0.179 Å−1

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#raps


8 Fourier-Shell correlation i○

This section was not generated. No FSC curve or half-maps provided.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validation


9 Map-model fit i○

This section contains information regarding the fit between EMDB map EMD-30642 and PDBmodel 7DD2. Per-residue inclusion information can be found in section 3 on page 8.

9.1 Map-model overlay i○

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.9 at50% transparency in yellow overlaid with a ribbon representation of the model coloured in blue.These images allow for the visual assessment of the quality of fit between the atomic model andthe map.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_fit

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_overlay


9.2 Atom inclusion i○

At the recommended contour level, 80% of all backbone atoms, 69% of all non-hydrogen atoms,are inside the map.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#atom_inclusion_by_contour

full wwpdb em validation report i · 2021. 1. 18. · full wwpdb em validation report ......

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