full wwpdb em validation report i - rcsb · 2020. 12. 14. · buster-report : 1.1.7 (2018)...

Full wwPDB EM Validation Report i○

Dec 13, 2020 – 07:47 PM EST

PDB ID : 6DM0EMDB ID : EMD-7960

Title : Open state GluA2 in complex with STZ and blocked by IEM-1460, after micellesignal subtraction

Authors : Twomey, E.C.; Yelshanskaya, M.V.; Vassilevski, A.A.; Sobolevsky, A.I.Deposited on : 2018-06-04

Resolution : 4.40 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.dev61Mogul : 1.8.5 (274361), CSD as541be (2020)

MolProbity : 4.02b-467buster-report : 1.1.7 (2018)

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) : 2.15.1

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



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

Full wwPDB EM Validation Report EMD-7960, 6DM0

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 4.40 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 A 1031

1 B 1031

1 C 1031

1 D 1031

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


2 Entry composition i○

There are 4 unique types of molecules in this entry. The entry contains 31095 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 Glutamate receptor 2,Voltage-dependent calcium channelgamma-2 subunit.

Mol Chain Residues Atoms AltConf Trace

1 A 984 Total C N O S7734 4980 1278 1435 41 0 0

1 B 985 Total C N O S7735 4981 1279 1434 41 0 0

1 C 984 Total C N O S7734 4980 1278 1435 41 0 0

1 D 985 Total C N O S7735 4981 1279 1434 41 0 0

There are 76 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 241 GLU ASN conflict UNP P19491A 382 LEU VAL conflict UNP P19491A ? - LEU deletion UNP P19491A ? - THR deletion UNP P19491A ? - GLU deletion UNP P19491A ? - LEU deletion UNP P19491A ? - PRO deletion UNP P19491A ? - SER deletion UNP P19491A 384 GLU GLY conflict UNP P19491A 385 ASP ASN conflict UNP P19491A 392 GLN ASN conflict UNP P19491A 999 GLY - linker UNP P19491A 1000 THR - linker UNP P19491A 1047 ASP ASN conflict UNP Q9Y698A 1208 THR - expression tag UNP Q9Y698A 1209 GLY - expression tag UNP Q9Y698A 1210 GLY - expression tag UNP Q9Y698A 1211 ALA - expression tag UNP Q9Y698A 1212 GLU - expression tag UNP Q9Y698B 241 GLU ASN conflict UNP P19491B 382 LEU VAL conflict UNP P19491

Continued on next page...

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


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

B ? - LEU deletion UNP P19491B ? - THR deletion UNP P19491B ? - GLU deletion UNP P19491B ? - LEU deletion UNP P19491B ? - PRO deletion UNP P19491B ? - SER deletion UNP P19491B 384 GLU GLY conflict UNP P19491B 385 ASP ASN conflict UNP P19491B 392 GLN ASN conflict UNP P19491B 999 GLY - linker UNP P19491B 1000 THR - linker UNP P19491B 1047 ASP ASN conflict UNP Q9Y698B 1208 THR - expression tag UNP Q9Y698B 1209 GLY - expression tag UNP Q9Y698B 1210 GLY - expression tag UNP Q9Y698B 1211 ALA - expression tag UNP Q9Y698B 1212 GLU - expression tag UNP Q9Y698C 241 GLU ASN conflict UNP P19491C 382 LEU VAL conflict UNP P19491C ? - LEU deletion UNP P19491C ? - THR deletion UNP P19491C ? - GLU deletion UNP P19491C ? - LEU deletion UNP P19491C ? - PRO deletion UNP P19491C ? - SER deletion UNP P19491C 384 GLU GLY conflict UNP P19491C 385 ASP ASN conflict UNP P19491C 392 GLN ASN conflict UNP P19491C 999 GLY - linker UNP P19491C 1000 THR - linker UNP P19491C 1047 ASP ASN conflict UNP Q9Y698C 1208 THR - expression tag UNP Q9Y698C 1209 GLY - expression tag UNP Q9Y698C 1210 GLY - expression tag UNP Q9Y698C 1211 ALA - expression tag UNP Q9Y698C 1212 GLU - expression tag UNP Q9Y698D 241 GLU ASN conflict UNP P19491D 382 LEU VAL conflict UNP P19491D ? - LEU deletion UNP P19491D ? - THR deletion UNP P19491D ? - GLU deletion UNP P19491D ? - LEU deletion UNP P19491



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

D ? - PRO deletion UNP P19491D ? - SER deletion UNP P19491D 384 GLU GLY conflict UNP P19491D 385 ASP ASN conflict UNP P19491D 392 GLN ASN conflict UNP P19491D 999 GLY - linker UNP P19491D 1000 THR - linker UNP P19491D 1047 ASP ASN conflict UNP Q9Y698D 1208 THR - expression tag UNP Q9Y698D 1209 GLY - expression tag UNP Q9Y698D 1210 GLY - expression tag UNP Q9Y698D 1211 ALA - expression tag UNP Q9Y698D 1212 GLU - expression tag UNP Q9Y698

• Molecule 2 is GLUTAMIC ACID (three-letter code: GLU) (formula: C5H9NO4).

Mol Chain Residues Atoms AltConf

2 A 1 Total C N O10 5 1 4 0

2 B 1 Total C N O10 5 1 4 0

2 C 1 Total C N O10 5 1 4 0

2 D 1 Total C N O10 5 1 4 0

• Molecule 3 is CYCLOTHIAZIDE (three-letter code: CYZ) (formula: C14H16ClN3O4S2).



3 A 1 Total C Cl N O S24 14 1 3 4 2 0

3 B 1 Total C Cl N O S24 14 1 3 4 2 0

3 C 1 Total C Cl N O S24 14 1 3 4 2 0

3 D 1 Total C Cl N O S24 14 1 3 4 2 0

• Molecule 4 is N,N,N-trimethyl-5-({[(3s,5s,7s)-tricyclo[3.3.1.1 3,7 ]decan-1-yl]methyl}amino)pentan-1-aminium (three-letter code: GZD) (formula: C19H37N2).



4 B 1 Total C N21 19 2 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: Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit

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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, C2 DepositorNumber of particles used 30849 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

) 55 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.141 DepositorMinimum map value -0.070 DepositorAverage map value 0.001 DepositorMap value standard deviation 0.005 DepositorRecommended contour level 0.04 DepositorMap size (Å) 324.0, 324.0, 324.0 wwPDBMap dimensions 300, 300, 300 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.08, 1.08, 1.08 Depositor

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


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: CYZ,GZD

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 A 0.38 0/7900 0.57 1/10670 (0.0%)1 B 0.37 0/7901 0.55 1/10672 (0.0%)1 C 0.38 0/7900 0.57 1/10670 (0.0%)1 D 0.37 0/7901 0.55 1/10672 (0.0%)All All 0.38 0/31602 0.56 4/42684 (0.0%)

Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying ifthe center is modelled as a planar moiety or with the opposite hand.A planarity outlier is detectedby checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of asidechain that are expected to be planar.

Mol Chain #Chirality outliers #Planarity outliers1 A 0 31 B 0 21 C 0 31 D 0 2All All 0 10

There are no bond length outliers.

All (4) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 A 1207 LEU CA-CB-CG 6.12 129.38 115.301 C 1207 LEU CA-CB-CG 6.08 129.28 115.301 B 596 LEU CA-CB-CG 5.37 127.64 115.301 D 596 LEU CA-CB-CG 5.36 127.62 115.30

There are no chirality outliers.

All (10) planarity outliers are listed below:

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

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


Mol Chain Res Type Group1 A 1177 TRP Peptide1 A 313 GLY Peptide1 A 632 PRO Peptide1 B 1005 ARG Peptide1 B 635 SER Peptide1 C 1177 TRP Peptide1 C 313 GLY Peptide1 C 632 PRO Peptide1 D 1005 ARG Peptide1 D 635 SER Peptide

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 A 7734 0 7713 58 01 B 7735 0 7708 70 01 C 7734 0 7713 60 01 D 7735 0 7708 72 02 A 10 0 5 1 02 B 10 0 5 1 02 C 10 0 5 1 02 D 10 0 5 1 03 A 24 0 11 1 03 B 24 0 11 0 03 C 24 0 11 1 03 D 24 0 11 0 04 B 21 0 0 2 0All All 31095 0 30906 248 0

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 4.

All (248) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:D:480:THR:HG1 2:D:1301:GLU:N 1.67 0.91Continued on next page...

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


Continued from previous page...


Clashoverlap (Å)

1:B:480:THR:HG1 2:B:1301:GLU:N 1.70 0.881:B:586:GLN:HE21 1:B:613:ILE:HD11 1.49 0.771:B:586:GLN:NE2 1:B:613:ILE:HD11 2.02 0.741:A:480:THR:HG1 2:A:1301:GLU:N 1.87 0.701:C:480:THR:HG1 2:C:1301:GLU:N 1.91 0.691:C:586:GLN:HE22 1:C:613:ILE:HG21 1.60 0.661:A:586:GLN:HE22 1:A:613:ILE:HG21 1.61 0.651:B:586:GLN:HE21 1:B:613:ILE:CD1 2.12 0.631:C:1029:THR:HG22 1:C:1031:TYR:H 1.64 0.621:B:589:CYS:SG 1:B:590:ASP:N 2.73 0.621:B:13:GLN:HA 1:B:44:THR:HB 1.83 0.611:D:589:CYS:SG 1:D:590:ASP:N 2.73 0.611:D:372:GLY:HA2 1:D:383:THR:HG23 1.84 0.601:B:372:GLY:HA2 1:B:383:THR:HG23 1.84 0.601:D:13:GLN:HA 1:D:44:THR:HB 1.83 0.601:C:1025:ILE:O 1:C:1029:THR:OG1 2.18 0.59

1:D:586:GLN:NE2 1:D:613:ILE:HD11 2.17 0.591:A:1036:ARG:HH11 1:A:1171:ASN:HA 1.68 0.58

1:A:13:GLN:HA 1:A:44:THR:HB 1.86 0.581:C:13:GLN:HA 1:C:44:THR:HB 1.86 0.581:A:375:SER:HB3 1:A:378:ASP:HB2 1.86 0.571:C:236:GLN:NE2 1:C:365:THR:O 2.38 0.571:A:112:GLN:HE21 1:A:352:LYS:HG2 1.70 0.561:A:236:GLN:NE2 1:A:365:THR:O 2.38 0.561:C:112:GLN:HE21 1:C:352:LYS:HG2 1.70 0.561:D:265:LEU:O 1:D:274:HIS:ND1 2.36 0.561:D:48:ASP:OD2 1:D:65:GLN:NE2 2.39 0.56

1:D:586:GLN:HE21 1:D:613:ILE:HD11 1.70 0.561:A:369:ARG:HH12 1:A:386:ASP:HB2 1.71 0.561:C:375:SER:HB3 1:C:378:ASP:HB2 1.86 0.561:A:1138:GLY:HA2 1:A:1141:PHE:HD2 1.72 0.551:C:693:VAL:HG21 1:C:702:TYR:HB2 1.88 0.551:B:1025:ILE:O 1:B:1029:THR:OG1 2.19 0.551:B:48:ASP:OD2 1:B:65:GLN:NE2 2.39 0.55

1:C:1036:ARG:HH11 1:C:1171:ASN:HA 1.71 0.551:B:185:GLU:OE2 1:B:213:LYS:NZ 2.38 0.551:B:637:GLU:O 1:B:640:SER:OG 2.22 0.551:C:236:GLN:HA 1:C:363:LEU:HD21 1.89 0.541:D:77:TYR:OH 1:D:101:PHE:O 2.22 0.541:B:586:GLN:OE1 4:B:1303:GZD:C17 2.56 0.541:C:494:PRO:O 3:C:1302:CYZ:N1 2.40 0.54





Clashoverlap (Å)

1:C:48:ASP:HB3 1:C:50:LEU:HD13 1.89 0.541:A:48:ASP:HB3 1:A:50:LEU:HD13 1.90 0.54

1:C:1138:GLY:HA2 1:C:1141:PHE:HD2 1.72 0.541:A:647:TYR:HB3 1:A:701:ALA:HB3 1.90 0.541:B:337:GLN:HE21 1:B:344:ASN:HD21 1.55 0.541:A:236:GLN:HA 1:A:363:LEU:HD21 1.90 0.541:D:1025:ILE:O 1:D:1029:THR:OG1 2.19 0.54

1:B:476:ILE:HG12 1:B:734:ILE:HD12 1.91 0.531:D:510:SER:OG 1:D:628:ARG:NH1 2.41 0.531:A:494:PRO:O 3:A:1302:CYZ:N1 2.41 0.53

1:B:328:GLU:OE2 1:B:331:ARG:NH2 2.40 0.531:B:510:SER:OG 1:B:628:ARG:NH1 2.41 0.531:D:266:GLU:HG2 1:D:268:LYS:H 1.73 0.531:B:77:TYR:OH 1:B:101:PHE:O 2.22 0.53

1:C:369:ARG:HH12 1:C:386:ASP:HB2 1.73 0.531:C:647:TYR:HB3 1:C:701:ALA:HB3 1.90 0.531:A:10:ASN:N 1:A:40:GLU:O 2.41 0.53

1:C:147:GLN:HE21 1:D:143:LEU:HD21 1.74 0.531:D:328:GLU:OE2 1:D:331:ARG:NH2 2.41 0.531:A:147:GLN:HE21 1:B:143:LEU:HD21 1.74 0.521:D:638:ASP:HA 1:D:641:LYS:HB2 1.91 0.521:C:10:ASN:N 1:C:40:GLU:O 2.42 0.52

1:D:1026:ALA:O 1:D:1178:SER:OG 2.28 0.521:B:1088:TYR:HD2 1:B:1091:ASP:HB2 1.74 0.521:A:693:VAL:HG21 1:A:702:TYR:HB2 1.92 0.521:D:1029:THR:HG22 1:D:1031:TYR:H 1.74 0.521:D:1068:LEU:HA 1:D:1073:LYS:HG3 1.90 0.521:D:476:ILE:HG12 1:D:734:ILE:HD12 1.91 0.521:A:405:TYR:HA 1:A:424:TYR:HB3 1.92 0.52

1:D:649:THR:HG22 1:D:703:LEU:HB2 1.92 0.521:D:1088:TYR:HD2 1:D:1091:ASP:HB2 1.74 0.511:A:190:ARG:HE 1:A:469:TYR:HB3 1.76 0.511:C:87:SER:OG 1:D:54:ASN:OD1 2.29 0.51

1:B:1068:LEU:HA 1:B:1073:LYS:HG3 1.92 0.511:A:628:ARG:NH2 1:A:780:SER:O 2.43 0.511:B:266:GLU:HG2 1:B:268:LYS:H 1.75 0.511:D:185:GLU:OE2 1:D:213:LYS:NZ 2.38 0.511:D:112:GLN:HE21 1:D:352:LYS:HG2 1.75 0.511:B:112:GLN:HE21 1:B:352:LYS:HG2 1.75 0.501:B:649:THR:HG22 1:B:703:LEU:HB2 1.93 0.501:A:220:TYR:HB2 1:A:242:VAL:HG22 1.93 0.50





Clashoverlap (Å)

1:B:638:ASP:HA 1:B:641:LYS:HB2 1.92 0.501:A:48:ASP:OD2 1:A:65:GLN:NE2 2.43 0.501:B:109:PHE:HZ 1:B:327:VAL:HG22 1.76 0.501:D:174:ASP:O 1:D:178:ARG:NH1 2.45 0.50

1:C:628:ARG:NH2 1:C:780:SER:O 2.44 0.501:B:1026:ALA:O 1:B:1178:SER:OG 2.28 0.501:C:190:ARG:HE 1:C:469:TYR:HB3 1.76 0.501:A:113:MET:HB3 1:A:284:LEU:HD22 1.94 0.491:B:174:ASP:O 1:B:178:ARG:NH1 2.45 0.49

1:D:337:GLN:HE21 1:D:344:ASN:HD21 1.59 0.491:B:1029:THR:HG22 1:B:1031:TYR:H 1.76 0.49

1:B:99:PRO:HA 1:B:113:MET:HB2 1.95 0.491:C:113:MET:HB3 1:C:284:LEU:HD22 1.95 0.491:D:109:PHE:HZ 1:D:327:VAL:HG22 1.76 0.491:D:297:ARG:HG3 1:D:301:LYS:HE2 1.94 0.491:D:500:ILE:HB 1:D:727:LEU:HB2 1.93 0.491:C:48:ASP:OD2 1:C:65:GLN:NE2 2.43 0.491:D:99:PRO:HA 1:D:113:MET:HB2 1.95 0.491:C:1177:TRP:O 1:C:1179:PHE:N 2.46 0.491:C:231:ASP:O 1:C:234:LYS:NZ 2.44 0.491:B:500:ILE:HB 1:B:727:LEU:HB2 1.94 0.49

1:B:297:ARG:HG3 1:B:301:LYS:HE2 1.95 0.491:C:545:ARG:NE 1:C:571:PHE:O 2.42 0.491:A:638:ASP:HA 1:A:641:LYS:HB2 1.94 0.491:A:1025:ILE:O 1:A:1029:THR:OG1 2.22 0.48

1:B:232:LEU:HD23 1:B:363:LEU:HD22 1.95 0.481:C:220:TYR:HB2 1:C:242:VAL:HG22 1.94 0.481:C:638:ASP:HA 1:C:641:LYS:HB2 1.94 0.481:B:163:ILE:HD13 1:B:180:LEU:HD11 1.95 0.481:D:294:GLU:HG2 1:D:336:VAL:HG13 1.95 0.481:D:232:LEU:HD23 1:D:363:LEU:HD22 1.95 0.481:A:1177:TRP:O 1:A:1179:PHE:N 2.46 0.481:D:163:ILE:HD13 1:D:180:LEU:HD11 1.95 0.481:B:401:LEU:HD23 1:B:406:VAL:HG12 1.95 0.481:A:87:SER:OG 1:B:54:ASN:OD1 2.29 0.481:A:231:ASP:O 1:A:234:LYS:NZ 2.43 0.481:B:722:LYS:NZ 1:B:724:GLY:O 2.47 0.481:C:1069:GLU:H 1:C:1073:LYS:HG2 1.79 0.481:A:681:VAL:O 1:A:700:TYR:OH 2.27 0.48

1:D:348:ASP:OD1 1:D:351:GLY:N 2.44 0.471:D:401:LEU:HD23 1:D:406:VAL:HG12 1.95 0.47





Clashoverlap (Å)

1:A:1069:GLU:H 1:A:1073:LYS:HG2 1.80 0.471:B:14:ILE:HD13 1:B:43:LEU:HD23 1.95 0.471:B:348:ASP:OD1 1:B:351:GLY:N 2.45 0.471:B:294:GLU:HG2 1:B:336:VAL:HG13 1.95 0.471:D:14:ILE:HD13 1:D:43:LEU:HD23 1.97 0.471:A:586:GLN:HE22 1:A:613:ILE:HD13 1.80 0.471:D:586:GLN:HE21 1:D:613:ILE:CD1 2.26 0.471:D:1059:HIS:HB2 1:D:1068:LEU:HD23 1.97 0.461:C:326:GLY:HA2 1:C:329:ILE:HD12 1.98 0.461:D:196:CYS:HB3 1:D:200:LYS:HB2 1.96 0.461:B:196:CYS:HB3 1:B:200:LYS:HB2 1.96 0.461:D:11:SER:HG 1:D:44:THR:HG1 1.60 0.461:A:597:SER:HA 1:A:600:ILE:HG22 1.97 0.461:D:506:LYS:N 1:D:719:ASP:O 2.49 0.46

1:A:130:TRP:CD2 1:A:191:ARG:HD3 2.51 0.461:B:520:PRO:HG3 1:B:623:PHE:CG 2.51 0.461:C:793:ALA:HA 1:C:796:PHE:HD2 1.81 0.46

1:B:394:THR:HG22 1:B:439:LYS:HB3 1.98 0.461:C:597:SER:HA 1:C:600:ILE:HG22 1.97 0.461:C:657:GLU:OE2 1:C:661:ARG:NH2 2.49 0.461:D:637:GLU:O 1:D:640:SER:OG 2.22 0.46

1:A:657:GLU:OE2 1:A:661:ARG:NH2 2.49 0.461:B:1059:HIS:HB2 1:B:1068:LEU:HD23 1.99 0.451:B:265:LEU:O 1:B:274:HIS:ND1 2.44 0.45

1:D:394:THR:HG22 1:D:439:LYS:HB3 1.98 0.451:D:520:PRO:HG3 1:D:623:PHE:CG 2.51 0.451:A:326:GLY:HA2 1:A:329:ILE:HD12 1.97 0.451:B:506:LYS:N 1:B:719:ASP:O 2.49 0.451:D:722:LYS:NZ 1:D:724:GLY:O 2.47 0.451:B:375:SER:HB3 1:B:378:ASP:HB2 1.99 0.451:D:375:SER:HB3 1:D:378:ASP:HB2 1.97 0.451:C:1031:TYR:HB3 1:C:1059:HIS:NE2 2.32 0.451:C:130:TRP:CD2 1:C:191:ARG:HD3 2.50 0.451:D:375:SER:OG 1:D:376:GLU:OE1 2.35 0.451:A:793:ALA:HA 1:A:796:PHE:HD2 1.81 0.45

1:B:1150:ILE:HD13 1:C:800:VAL:HG21 1.99 0.451:C:249:ASP:OD1 1:C:359:ASN:ND2 2.50 0.451:C:348:ASP:OD1 1:C:352:LYS:N 2.50 0.451:B:596:LEU:HD13 1:B:597:SER:HB3 1.99 0.441:A:498:LEU:HD13 1:A:705:GLU:HB3 1.99 0.441:C:141:ARG:NH2 1:C:195:ASP:OD1 2.49 0.44





Clashoverlap (Å)

1:A:1002:LEU:HB3 1:A:1003:PHE:H 1.66 0.441:B:480:THR:O 1:B:485:ARG:NH1 2.49 0.44

1:C:400:ILE:HG21 1:C:450:TYR:HE1 1.81 0.441:D:480:THR:O 1:D:485:ARG:NH1 2.50 0.44

1:A:249:ASP:OD1 1:A:359:ASN:ND2 2.51 0.441:C:348:ASP:OD1 1:C:351:GLY:N 2.51 0.441:C:545:ARG:NH1 1:C:569:ASN:O 2.50 0.441:C:498:LEU:HD13 1:C:705:GLU:HB3 1.99 0.441:D:235:ILE:HG13 1:D:235:ILE:H 1.65 0.441:A:348:ASP:OD1 1:A:351:GLY:N 2.50 0.431:A:545:ARG:NH1 1:A:569:ASN:O 2.50 0.431:B:611:ILE:HD11 1:C:517:PHE:HB2 2.00 0.431:D:596:LEU:HD13 1:D:597:SER:HB3 1.99 0.431:A:54:ASN:OD1 1:B:87:SER:OG 2.30 0.431:D:1125:GLU:HA 1:D:1128:LYS:HB3 2.00 0.431:A:800:VAL:HG21 1:D:1150:ILE:HD13 2.00 0.431:D:510:SER:OG 1:D:628:ARG:O 2.36 0.431:D:105:GLY:O 1:D:107:HIS:ND1 2.52 0.43

1:C:1002:LEU:HB3 1:C:1003:PHE:H 1.65 0.431:D:1031:TYR:HB3 1:D:1059:HIS:NE2 2.34 0.431:A:400:ILE:HG21 1:A:450:TYR:HE1 1.83 0.431:B:105:GLY:O 1:B:107:HIS:ND1 2.52 0.431:C:719:ASP:N 1:C:719:ASP:OD1 2.52 0.431:A:1106:PHE:O 1:A:1147:SER:OG 2.35 0.431:A:794:GLY:HA2 1:A:797:TYR:HD2 1.84 0.431:C:77:TYR:HE1 1:C:98:THR:HG21 1.84 0.431:B:375:SER:OG 1:B:376:GLU:OE1 2.36 0.431:C:681:VAL:O 1:C:700:TYR:OH 2.26 0.43

1:D:400:ILE:HG21 1:D:450:TYR:HE1 1.84 0.431:A:348:ASP:OD1 1:A:352:LYS:N 2.51 0.421:B:247:ILE:HG22 1:B:358:ILE:HG12 2.01 0.421:C:330:GLU:HA 1:C:333:LEU:HD12 2.01 0.421:D:636:ALA:O 1:D:638:ASP:N 2.42 0.42

1:A:517:PHE:HB2 1:D:611:ILE:HD11 2.00 0.421:C:1106:PHE:O 1:C:1147:SER:OG 2.35 0.42

1:C:586:GLN:HE22 1:C:613:ILE:HD13 1.83 0.421:B:1125:GLU:HA 1:B:1128:LYS:HB3 1.99 0.421:A:77:TYR:HE1 1:A:98:THR:HG21 1.84 0.421:B:235:ILE:HD13 1:B:242:VAL:HG21 2.01 0.421:C:633:ILE:H 1:C:633:ILE:HG12 1.48 0.42

1:D:13:GLN:HB3 1:D:70:VAL:HG12 2.01 0.42Continued on next page...




Clashoverlap (Å)

1:C:794:GLY:HA2 1:C:797:TYR:HD2 1.84 0.421:A:69:GLY:HA2 1:A:309:ARG:HH12 1.85 0.421:D:177:TYR:HD2 1:D:207:GLN:HG3 1.84 0.421:B:177:TYR:HD2 1:B:207:GLN:HG3 1.85 0.421:B:48:ASP:HB3 1:B:50:LEU:HD13 2.01 0.42

1:A:143:LEU:HD21 1:B:147:GLN:HE21 1.85 0.411:B:98:THR:HA 1:B:99:PRO:HD3 1.88 0.41

1:C:143:LEU:HD21 1:D:147:GLN:HE21 1.85 0.411:D:247:ILE:HG22 1:D:358:ILE:HG12 2.01 0.411:A:306:ILE:HG13 1:A:306:ILE:H 1.78 0.411:B:77:TYR:HE1 1:B:98:THR:HG21 1.85 0.411:D:48:ASP:HB3 1:D:50:LEU:HD13 2.02 0.411:D:640:SER:HB2 1:D:669:LYS:HD3 2.02 0.411:D:77:TYR:HE1 1:D:98:THR:HG21 1.85 0.411:B:400:ILE:HG21 1:B:450:TYR:HE1 1.86 0.411:B:784:THR:OG1 1:B:785:SER:N 2.53 0.411:C:375:SER:OG 1:C:376:GLU:N 2.54 0.411:B:209:ILE:HG13 1:B:214:HIS:CD2 2.55 0.411:B:636:ALA:O 1:B:638:ASP:N 2.43 0.411:B:13:GLN:HB3 1:B:70:VAL:HG12 2.01 0.411:C:54:ASN:OD1 1:D:87:SER:OG 2.30 0.411:C:624:LEU:HD13 1:C:624:LEU:HA 1.91 0.411:D:209:ILE:HG13 1:D:214:HIS:CD2 2.55 0.411:D:711:TYR:HB2 1:D:767:TRP:HE1 1.85 0.411:A:150:LEU:HD23 1:A:150:LEU:HA 1.91 0.411:A:330:GLU:HA 1:A:333:LEU:HD12 2.01 0.41

1:D:1101:ARG:HG3 1:D:1158:ALA:HB3 2.01 0.411:D:1081:HIS:HB3 1:D:1098:ARG:HD2 2.03 0.411:D:235:ILE:HD13 1:D:242:VAL:HG21 2.02 0.411:B:1101:ARG:HG3 1:B:1158:ALA:HB3 2.02 0.411:C:109:PHE:HZ 1:C:327:VAL:HG22 1.86 0.411:A:109:PHE:HZ 1:A:327:VAL:HG22 1.86 0.411:A:334:LYS:HA 1:A:347:PHE:HD2 1.85 0.411:C:306:ILE:H 1:C:306:ILE:HG13 1.78 0.40

1:C:69:GLY:HA2 1:C:309:ARG:HH12 1.86 0.401:A:1059:HIS:H 1:A:1067:CYS:HA 1.86 0.401:B:334:LYS:HA 1:B:347:PHE:HD2 1.87 0.401:B:586:GLN:CD 4:B:1303:GZD:C17 2.89 0.401:D:143:LEU:HD23 1:D:146:LEU:HD23 2.03 0.401:B:143:LEU:HD23 1:B:146:LEU:HD23 2.03 0.401:A:14:ILE:HD13 1:A:43:LEU:HD23 2.04 0.40





Clashoverlap (Å)

1:A:375:SER:OG 1:A:376:GLU:N 2.54 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 A 974/1031 (94%) 888 (91%) 81 (8%) 5 (0%) 29 68

1 B 975/1031 (95%) 889 (91%) 83 (8%) 3 (0%) 41 76

1 C 974/1031 (94%) 888 (91%) 81 (8%) 5 (0%) 29 68

1 D 975/1031 (95%) 890 (91%) 82 (8%) 3 (0%) 41 76

All All 3898/4124 (94%) 3555 (91%) 327 (8%) 16 (0%) 38 72

All (16) Ramachandran outliers are listed below:

Mol Chain Res Type1 A 633 ILE1 A 1178 SER1 B 1171 ASN1 C 633 ILE1 C 1178 SER1 D 1171 ASN1 A 632 PRO1 A 634 GLU1 B 636 ALA1 B 637 GLU1 C 632 PRO1 C 634 GLU1 D 636 ALA1 D 637 GLU


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

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


Continued from previous page...Mol Chain Res Type1 A 314 ASP1 C 314 ASP

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 A 832/873 (95%) 822 (99%) 10 (1%) 71 84

1 B 831/873 (95%) 826 (99%) 5 (1%) 86 92

1 C 832/873 (95%) 822 (99%) 10 (1%) 71 84

1 D 831/873 (95%) 826 (99%) 5 (1%) 86 92

All All 3326/3492 (95%) 3296 (99%) 30 (1%) 79 88

All (30) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 198 ARG1 A 308 ARG1 A 309 ARG1 A 334 LYS1 A 355 ASN1 A 453 ARG1 A 578 TRP1 A 629 MET1 A 1005 ARG1 A 1203 ARG1 B 453 ARG1 B 506 LYS1 B 628 ARG1 B 747 ASN1 B 1101 ARG1 C 198 ARG1 C 308 ARG1 C 309 ARG1 C 334 LYS


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


Continued from previous page...Mol Chain Res Type1 C 355 ASN1 C 453 ARG1 C 578 TRP1 C 629 MET1 C 1005 ARG1 C 1203 ARG1 D 453 ARG1 D 506 LYS1 D 628 ARG1 D 747 ASN1 D 1101 ARG

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (17)such sidechains are listed below:

Mol Chain Res Type1 A 147 GLN1 A 214 HIS1 A 355 ASN1 B 24 GLN1 B 337 GLN1 B 412 HIS1 B 586 GLN1 B 747 ASN1 B 791 ASN1 C 147 GLN1 C 355 ASN1 D 24 GLN1 D 337 GLN1 D 412 HIS1 D 586 GLN1 D 747 ASN1 D 791 ASN

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.

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

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


5.5 Carbohydrates i○

There are no monosaccharides in this entry.

5.6 Ligand geometry i○

9 ligands are modelled in this entry.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are defined in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2

3 CYZ B 1302 - 26,27,27 7.10 19 (73%) 38,44,44 4.58 20 (52%)3 CYZ D 1302 - 26,27,27 7.09 19 (73%) 38,44,44 4.58 20 (52%)3 CYZ C 1302 - 26,27,27 7.07 20 (76%) 38,44,44 4.53 18 (47%)3 CYZ A 1302 - 26,27,27 7.08 20 (76%) 38,44,44 4.53 18 (47%)4 GZD B 1303 - 23,23,23 0.92 0 34,34,34 1.98 7 (20%)2 GLU D 1301 - 2,9,9 0.30 0 2,11,11 0.72 02 GLU C 1301 - 2,9,9 0.23 0 2,11,11 0.53 02 GLU B 1301 - 2,9,9 0.29 0 2,11,11 0.70 02 GLU A 1301 - 2,9,9 0.25 0 2,11,11 0.53 0

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.’-’ means no outliers of that kind were identified.

Mol Type Chain Res Link Chirals Torsions Rings3 CYZ B 1302 - - 0/6/42/42 0/5/4/43 CYZ D 1302 - - 0/6/42/42 0/5/4/43 CYZ C 1302 - - 0/6/42/42 0/5/4/43 CYZ A 1302 - - 0/6/42/42 0/5/4/44 GZD B 1303 - - 7/12/39/39 0/4/3/32 GLU D 1301 - - 0/3/9/9 -2 GLU C 1301 - - 0/3/9/9 -2 GLU B 1301 - - 0/3/9/9 -2 GLU A 1301 - - 0/3/9/9 -




All (78) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 B 1302 CYZ C2-C1 -19.42 1.13 1.553 D 1302 CYZ C2-C1 -19.40 1.13 1.553 C 1302 CYZ C2-C1 -19.40 1.13 1.553 A 1302 CYZ C2-C1 -19.38 1.13 1.553 B 1302 CYZ C9-S1 -14.21 1.63 1.753 D 1302 CYZ C9-S1 -14.19 1.63 1.753 A 1302 CYZ C9-S1 -14.06 1.63 1.753 C 1302 CYZ C9-S1 -14.02 1.63 1.753 D 1302 CYZ C2-C3 -13.99 1.13 1.513 B 1302 CYZ C2-C3 -13.97 1.13 1.513 A 1302 CYZ C2-C3 -13.91 1.13 1.513 C 1302 CYZ C2-C3 -13.90 1.13 1.513 A 1302 CYZ C10-N2 9.45 1.56 1.393 C 1302 CYZ C10-N2 9.43 1.56 1.393 D 1302 CYZ C10-N2 9.41 1.56 1.393 B 1302 CYZ C10-N2 9.39 1.56 1.393 B 1302 CYZ C4-C3 9.29 1.59 1.323 C 1302 CYZ C4-C3 9.27 1.59 1.323 D 1302 CYZ C4-C3 9.26 1.59 1.323 A 1302 CYZ C4-C3 9.22 1.59 1.323 B 1302 CYZ C5-C4 -8.89 1.08 1.503 D 1302 CYZ C5-C4 -8.88 1.08 1.503 A 1302 CYZ C5-C4 -8.81 1.08 1.503 C 1302 CYZ C5-C4 -8.81 1.08 1.503 B 1302 CYZ S2-N3 7.52 1.75 1.603 D 1302 CYZ S2-N3 7.51 1.75 1.603 A 1302 CYZ S2-N3 7.50 1.75 1.603 C 1302 CYZ S2-N3 7.47 1.75 1.603 D 1302 CYZ C6-C5 -6.86 1.12 1.513 C 1302 CYZ C6-C5 -6.84 1.12 1.513 B 1302 CYZ C6-C5 -6.84 1.12 1.513 A 1302 CYZ C6-C5 -6.83 1.12 1.513 C 1302 CYZ C6-C1 -5.10 1.39 1.533 A 1302 CYZ C6-C1 -5.08 1.39 1.533 C 1302 CYZ C8-N1 -5.04 1.40 1.463 B 1302 CYZ C6-C1 -4.99 1.39 1.533 D 1302 CYZ C6-C1 -4.98 1.39 1.533 A 1302 CYZ C8-N1 -4.98 1.40 1.463 B 1302 CYZ C12-S2 4.84 1.83 1.773 D 1302 CYZ C12-S2 4.79 1.83 1.773 D 1302 CYZ C8-N1 -4.73 1.41 1.463 B 1302 CYZ C8-N1 -4.68 1.41 1.46



Continued from previous page...Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 A 1302 CYZ O2-S1 4.57 1.48 1.433 C 1302 CYZ C12-S2 4.55 1.83 1.773 A 1302 CYZ C12-S2 4.55 1.83 1.773 C 1302 CYZ O2-S1 4.54 1.48 1.433 D 1302 CYZ O2-S1 4.46 1.48 1.433 B 1302 CYZ C10-C9 -4.44 1.34 1.403 B 1302 CYZ O2-S1 4.41 1.48 1.433 D 1302 CYZ C10-C9 -4.38 1.34 1.403 A 1302 CYZ C10-C9 -4.33 1.34 1.403 C 1302 CYZ C10-C9 -4.32 1.34 1.403 D 1302 CYZ O3-S2 3.97 1.51 1.433 B 1302 CYZ O3-S2 3.92 1.51 1.433 A 1302 CYZ O3-S2 3.81 1.50 1.433 C 1302 CYZ O3-S2 3.79 1.50 1.433 B 1302 CYZ C7-C5 -3.56 1.31 1.513 A 1302 CYZ C7-C5 -3.55 1.31 1.513 D 1302 CYZ C7-C5 -3.55 1.31 1.513 C 1302 CYZ C7-C5 -3.55 1.31 1.513 C 1302 CYZ C8-N2 3.51 1.50 1.463 A 1302 CYZ C8-N2 3.50 1.50 1.463 D 1302 CYZ C8-N2 3.40 1.50 1.463 B 1302 CYZ C8-N2 3.38 1.50 1.463 D 1302 CYZ C13-CL 2.89 1.80 1.733 B 1302 CYZ C13-CL 2.88 1.80 1.733 A 1302 CYZ C13-CL 2.84 1.80 1.733 C 1302 CYZ C13-CL 2.78 1.80 1.733 A 1302 CYZ S1-N1 -2.65 1.59 1.623 B 1302 CYZ S1-N1 -2.65 1.59 1.623 D 1302 CYZ S1-N1 -2.63 1.59 1.623 C 1302 CYZ S1-N1 -2.61 1.59 1.623 A 1302 CYZ C11-C12 -2.26 1.35 1.393 C 1302 CYZ O4-S2 2.19 1.47 1.433 A 1302 CYZ O4-S2 2.18 1.47 1.433 C 1302 CYZ C11-C12 -2.17 1.35 1.393 D 1302 CYZ O4-S2 2.17 1.47 1.433 B 1302 CYZ O4-S2 2.13 1.47 1.43

All (83) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 A 1302 CYZ C1-C2-C3 18.83 137.39 106.923 D 1302 CYZ C1-C2-C3 18.81 137.36 106.92



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 B 1302 CYZ C1-C2-C3 18.80 137.34 106.923 C 1302 CYZ C1-C2-C3 18.80 137.34 106.923 B 1302 CYZ O4-S2-O3 -10.74 101.10 118.763 D 1302 CYZ O4-S2-O3 -10.73 101.12 118.763 D 1302 CYZ C9-S1-N1 10.58 116.92 103.433 B 1302 CYZ C9-S1-N1 10.52 116.85 103.433 C 1302 CYZ O4-S2-O3 -10.31 101.82 118.763 A 1302 CYZ O4-S2-O3 -10.28 101.86 118.763 A 1302 CYZ C9-S1-N1 10.06 116.27 103.433 C 1302 CYZ C9-S1-N1 10.05 116.25 103.433 A 1302 CYZ C7-C2-C1 -6.09 87.45 101.073 C 1302 CYZ C7-C2-C1 -6.08 87.46 101.073 D 1302 CYZ C7-C2-C1 -5.93 87.81 101.073 B 1302 CYZ C7-C2-C1 -5.91 87.84 101.073 B 1302 CYZ O2-S1-O1 -5.90 112.44 118.463 D 1302 CYZ O2-S1-O1 -5.89 112.45 118.464 B 1303 GZD C21-C12-C17 5.73 113.00 108.463 C 1302 CYZ C2-C1-C8 -5.44 107.07 114.813 A 1302 CYZ C2-C1-C8 -5.42 107.11 114.813 A 1302 CYZ O2-S1-O1 -5.38 112.97 118.463 C 1302 CYZ O2-S1-O1 -5.36 112.99 118.464 B 1303 GZD C12-C17-C16 -5.17 106.77 110.443 B 1302 CYZ C2-C1-C8 -4.55 108.34 114.813 D 1302 CYZ C2-C1-C8 -4.52 108.38 114.814 B 1303 GZD C12-C11-N10 -3.98 107.70 114.213 D 1302 CYZ C7-C2-C3 -3.91 89.08 99.693 B 1302 CYZ C7-C2-C3 -3.89 89.12 99.693 B 1302 CYZ O3-S2-N3 3.88 113.11 107.363 D 1302 CYZ O3-S2-N3 3.87 113.10 107.364 B 1303 GZD C12-C13-C14 -3.80 107.75 110.443 C 1302 CYZ C6-C5-C4 3.79 132.26 101.523 A 1302 CYZ C6-C5-C4 3.78 132.18 101.523 B 1302 CYZ C6-C5-C4 3.76 131.99 101.523 D 1302 CYZ C6-C5-C4 3.75 131.92 101.524 B 1303 GZD C12-C21-C19 -3.74 107.79 110.443 A 1302 CYZ C7-C2-C3 -3.53 90.11 99.693 C 1302 CYZ C7-C2-C3 -3.52 90.13 99.693 C 1302 CYZ O3-S2-N3 3.42 112.44 107.363 A 1302 CYZ O3-S2-N3 3.41 112.43 107.363 C 1302 CYZ O4-S2-N3 3.17 112.06 107.363 A 1302 CYZ O4-S2-N3 3.15 112.04 107.363 B 1302 CYZ O4-S2-N3 3.13 112.00 107.36



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 D 1302 CYZ O4-S2-N3 3.08 111.93 107.363 A 1302 CYZ O4-S2-C12 2.99 111.67 107.293 C 1302 CYZ O4-S2-C12 2.98 111.65 107.293 D 1302 CYZ O4-S2-C12 2.89 111.52 107.293 B 1302 CYZ O4-S2-C12 2.86 111.48 107.293 C 1302 CYZ C12-C11-C9 -2.72 118.12 120.943 C 1302 CYZ C11-C12-C13 2.70 121.14 118.273 A 1302 CYZ C12-C11-C9 -2.70 118.15 120.943 A 1302 CYZ C11-C12-C13 2.69 121.13 118.273 C 1302 CYZ O1-S1-C9 -2.66 106.01 109.293 A 1302 CYZ O1-S1-C9 -2.65 106.01 109.293 C 1302 CYZ C2-C3-C4 -2.61 101.29 107.993 A 1302 CYZ C2-C3-C4 -2.60 101.31 107.994 B 1303 GZD C3-N2-C4 -2.58 102.34 108.973 D 1302 CYZ O2-S1-C9 -2.51 106.19 109.293 B 1302 CYZ O2-S1-C9 -2.50 106.21 109.293 D 1302 CYZ C12-C13-CL -2.49 119.67 121.493 B 1302 CYZ C11-C12-C13 2.46 120.89 118.273 B 1302 CYZ C2-C3-C4 -2.46 101.68 107.993 B 1302 CYZ O1-S1-C9 -2.45 106.26 109.293 D 1302 CYZ C2-C3-C4 -2.44 101.73 107.993 B 1302 CYZ C12-C13-CL -2.44 119.71 121.493 B 1302 CYZ C12-C11-C9 -2.40 118.46 120.943 D 1302 CYZ C11-C12-C13 2.39 120.81 118.273 D 1302 CYZ O1-S1-C9 -2.39 106.35 109.293 D 1302 CYZ C12-C11-C9 -2.33 118.54 120.943 B 1302 CYZ C13-C12-S2 -2.30 120.57 123.493 C 1302 CYZ C6-C1-C8 -2.28 108.56 114.403 A 1302 CYZ C6-C1-C8 -2.28 108.57 114.403 D 1302 CYZ C6-C1-C8 -2.28 108.58 114.403 B 1302 CYZ C6-C1-C8 -2.26 108.63 114.403 D 1302 CYZ C13-C12-S2 -2.25 120.64 123.493 C 1302 CYZ C13-C12-S2 -2.16 120.75 123.493 A 1302 CYZ C12-C13-CL -2.15 119.92 121.493 C 1302 CYZ C12-C13-CL -2.14 119.93 121.493 A 1302 CYZ C13-C12-S2 -2.11 120.81 123.493 D 1302 CYZ O3-S2-C12 2.08 110.34 107.293 B 1302 CYZ O3-S2-C12 2.08 110.33 107.294 B 1303 GZD C21-C12-C13 2.04 110.07 108.46

There are no chirality outliers.

All (7) torsion outliers are listed below:


Mol Chain Res Type Atoms4 B 1303 GZD N2-C5-C6-C74 B 1303 GZD C8-C9-N10-C114 B 1303 GZD C6-C7-C8-C94 B 1303 GZD C5-C6-C7-C84 B 1303 GZD C7-C8-C9-N104 B 1303 GZD C6-C5-N2-C34 B 1303 GZD C6-C5-N2-C1

There are no ring outliers.

7 monomers are involved in 8 short contacts:

Mol Chain Res Type Clashes Symm-Clashes3 C 1302 CYZ 1 03 A 1302 CYZ 1 04 B 1303 GZD 2 02 D 1301 GLU 1 02 C 1301 GLU 1 02 B 1301 GLU 1 02 A 1301 GLU 1 0

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identified as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identified by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identified rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not find sufficientequivalents in the CSD to analyse the geometry.


Ligand CYZ B 1302

Bond lengths Bond angles

Torsions Rings


Ligand CYZ D 1302


Torsions Rings


Ligand CYZ C 1302


Torsions Rings


Ligand CYZ A 1302


Torsions Rings

Ligand GZD B 1303


Torsions Rings

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#polymer_linkage


6 Map visualisation i○

This section contains visualisations of the EMDB entry EMD-7960. 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: 150 Y Index: 150 Z Index: 150

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: 154 Y Index: 145 Z Index: 196

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 0.04.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 180 nm3; this corresponds to an approximatemass of 163 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 0.227 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-7960 and PDBmodel 6DM0. 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 0.04 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, 81% of all backbone atoms, 54% 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 - rcsb · 2020. 12. 14. · buster-report : 1.1.7 (2018)...

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