Full wwPDB EM Validation Report i○
Dec 13, 2020 – 06:37 AM EST
PDB ID : 6CRZEMDB ID : EMD-7577
Title : SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, C3 symmetryAuthors : Kirchdoerfer, R.N.; Wang, N.; Pallesen, J.; Turner, H.L.; Cottrell, C.A.;
McLellan, J.S.; Ward, A.B.Deposited on : 2018-03-19
Resolution : 3.30 Å(reported)Based on initial models : 5I08, 5X4S, 2AJF
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-467Percentile 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
Page 2 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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 3.30 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 1215
1 B 1215
1 C 1215
2 D 3
2 F 3
2 J 3
2 K 3
2 M 3Continued on next page...
Page 3 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...Mol Chain Length Quality of chain
2 N 3
2 R 3
2 T 3
2 U 3
3 E 4
4 G 2
4 H 2
4 I 2
4 L 2
4 O 2
4 P 2
4 Q 2
4 V 2
5 S 4
Page 4 Full wwPDB EM Validation Report EMD-7577, 6CRZ
2 Entry composition i○
There are 6 unique types of molecules in this entry. The entry contains 25909 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,Fibritin.
Mol Chain Residues Atoms AltConf Trace
1 A 1068 Total C N O S8339 5328 1379 1586 46 0 0
1 B 1068 Total C N O S8342 5331 1379 1586 46 0 0
1 C 1069 Total C N O S8343 5329 1380 1588 46 0 0
There are 42 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA 577 ALA SER conflict UNP P59594A 968 PRO LYS engineered mutation UNP P59594A 969 PRO VAL engineered mutation UNP P59594A 1191 GLY - linker UNP P59594A 1192 SER ALA linker UNP D9IEJ2A 1220 GLY - expression tag UNP D9IEJ2A 1221 ARG - expression tag UNP D9IEJ2A 1222 SER - expression tag UNP D9IEJ2A 1223 LEU - expression tag UNP D9IEJ2A 1224 GLU - expression tag UNP D9IEJ2A 1225 VAL - expression tag UNP D9IEJ2A 1226 LEU - expression tag UNP D9IEJ2A 1227 PHE - expression tag UNP D9IEJ2A 1228 GLN - expression tag UNP D9IEJ2B 577 ALA SER conflict UNP P59594B 968 PRO LYS engineered mutation UNP P59594B 969 PRO VAL engineered mutation UNP P59594B 1191 GLY - linker UNP P59594B 1192 SER ALA linker UNP D9IEJ2B 1220 GLY - expression tag UNP D9IEJ2B 1221 ARG - expression tag UNP D9IEJ2B 1222 SER - expression tag UNP D9IEJ2B 1223 LEU - expression tag UNP D9IEJ2B 1224 GLU - expression tag UNP D9IEJ2
Continued on next page...
Page 5 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...Chain Residue Modelled Actual Comment Reference
B 1225 VAL - expression tag UNP D9IEJ2B 1226 LEU - expression tag UNP D9IEJ2B 1227 PHE - expression tag UNP D9IEJ2B 1228 GLN - expression tag UNP D9IEJ2C 577 ALA SER conflict UNP P59594C 968 PRO LYS engineered mutation UNP P59594C 969 PRO VAL engineered mutation UNP P59594C 1191 GLY - linker UNP P59594C 1192 SER ALA linker UNP D9IEJ2C 1220 GLY - expression tag UNP D9IEJ2C 1221 ARG - expression tag UNP D9IEJ2C 1222 SER - expression tag UNP D9IEJ2C 1223 LEU - expression tag UNP D9IEJ2C 1224 GLU - expression tag UNP D9IEJ2C 1225 VAL - expression tag UNP D9IEJ2C 1226 LEU - expression tag UNP D9IEJ2C 1227 PHE - expression tag UNP D9IEJ2C 1228 GLN - expression tag UNP D9IEJ2
• Molecule 2 is an oligosaccharide called beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose.
Mol Chain Residues Atoms AltConf Trace
2 D 3 Total C N O39 22 2 15 0 0
2 F 3 Total C N O39 22 2 15 0 0
2 J 3 Total C N O39 22 2 15 0 0
2 K 3 Total C N O39 22 2 15 0 0
2 M 3 Total C N O39 22 2 15 0 0
2 N 3 Total C N O39 22 2 15 0 0
2 R 3 Total C N O39 22 2 15 0 0
Continued on next page...
Page 6 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...Mol Chain Residues Atoms AltConf Trace
2 T 3 Total C N O39 22 2 15 0 0
2 U 3 Total C N O39 22 2 15 0 0
• Molecule 3 is an oligosaccharide called alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose.
Mol Chain Residues Atoms AltConf Trace
3 E 4 Total C N O50 28 2 20 0 0
• Molecule 4 is an oligosaccharide called 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose.
Mol Chain Residues Atoms AltConf Trace
4 G 2 Total C N O28 16 2 10 0 0
4 H 2 Total C N O28 16 2 10 0 0
4 I 2 Total C N O28 16 2 10 0 0
4 L 2 Total C N O28 16 2 10 0 0
4 O 2 Total C N O28 16 2 10 0 0
4 P 2 Total C N O28 16 2 10 0 0
4 Q 2 Total C N O28 16 2 10 0 0
4 V 2 Total C N O28 16 2 10 0 0
Page 7 Full wwPDB EM Validation Report EMD-7577, 6CRZ
• Molecule 5 is an oligosaccharide called alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose.
Mol Chain Residues Atoms AltConf Trace
5 S 4 Total C N O50 28 2 20 0 0
• Molecule 6 is 2-acetamido-2-deoxy-beta-D-glucopyranose (three-letter code: NAG) (formula:C8H15NO6).
Mol Chain Residues Atoms AltConf
6 A 1 Total C N O56 32 4 20 0
6 A 1 Total C N O56 32 4 20 0
6 A 1 Total C N O56 32 4 20 0
6 A 1 Total C N O56 32 4 20 0
6 B 1 Total C N O70 40 5 25 0
6 B 1 Total C N O70 40 5 25 0
Continued on next page...
Page 8 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...Mol Chain Residues Atoms AltConf
6 B 1 Total C N O70 40 5 25 0
6 B 1 Total C N O70 40 5 25 0
6 B 1 Total C N O70 40 5 25 0
6 C 1 Total C N O84 48 6 30 0
6 C 1 Total C N O84 48 6 30 0
6 C 1 Total C N O84 48 6 30 0
6 C 1 Total C N O84 48 6 30 0
6 C 1 Total C N O84 48 6 30 0
6 C 1 Total C N O84 48 6 30 0
Page 9 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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,Fibritin
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Page 10 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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Page 13 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain D:
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• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Page 14 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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�BM
A3�
• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain J:
NAG1
�NA
G2�
BMA3
�
• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain K:
NAG1
�NA
G2�
BMA3
�
• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain M:
NAG1
�NA
G2�
BMA3
�
• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain N:
NAG1
NAG2
�BM
A3�
• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain R:
NAG1
�NA
G2�
BMA3
�
Page 15 Full wwPDB EM Validation Report EMD-7577, 6CRZ
• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain T:
NAG1
�NA
G2�
BMA3
�
• Molecule 2: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain U:
NAG1
�NA
G2�
BMA3
�
• Molecule 3: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain E:
NAG1
�NA
G2�
BMA3
�MA
N4�
• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain G:
NAG1
�NA
G2�
• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain H:
NAG1
�NA
G2�
• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain I:
Page 16 Full wwPDB EM Validation Report EMD-7577, 6CRZ
NAG1
�NA
G2�
• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain L:
NAG1
�NA
G2�
• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain O:
NAG1
�NA
G2�
• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain P:
NAG1
�NA
G2�
• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain Q:
NAG1
�NA
G2�
• Molecule 4: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Chain V:
NAG1
�NA
G2�
• Molecule 5: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Page 17 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Chain S:NA
G1�
NAG2
�BM
A3�
MAN4
�
Page 18 Full wwPDB EM Validation Report EMD-7577, 6CRZ
4 Experimental information i○
Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C3 DepositorNumber of particles used 162177 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
) 65 DepositorMinimum defocus (nm) 1200 DepositorMaximum defocus (nm) 2200 DepositorMagnification 29000 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.374 DepositorMinimum map value -0.191 DepositorAverage map value -0.000 DepositorMap value standard deviation 0.008 DepositorRecommended contour level 0.069 DepositorMap size (Å) 329.59998, 329.59998, 329.59998 wwPDBMap dimensions 320, 320, 320 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.03, 1.03, 1.03 Depositor
Page 19 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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:BMA, NAG, MAN
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 0.37 0/8538 0.59 2/11617 (0.0%)1 B 0.37 0/8541 0.59 1/11622 (0.0%)1 C 0.37 0/8541 0.59 0/11621All All 0.37 0/25620 0.59 3/34860 (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 11 B 0 11 C 0 3All All 0 5
There are no bond length outliers.
All (3) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 B 1070 TYR C-N-CA 5.77 136.12 121.701 A 355 LEU CA-CB-CG 5.28 127.44 115.301 A 898 LEU CB-CG-CD1 -5.25 102.08 111.00
There are no chirality outliers.
All (5) planarity outliers are listed below:
Mol Chain Res Type Group1 A 85 ASP Peptide
Continued on next page...
Page 20 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...Mol Chain Res Type Group1 B 1080 ASN Peptide1 C 207 ARG Peptide1 C 525 VAL Peptide1 C 85 ASP 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 8339 0 8083 133 01 B 8342 0 8088 113 01 C 8343 0 8086 118 02 D 39 0 34 0 02 F 39 0 34 0 02 J 39 0 34 0 02 K 39 0 34 0 02 M 39 0 34 0 02 N 39 0 34 0 02 R 39 0 34 0 02 T 39 0 34 0 02 U 39 0 34 0 03 E 50 0 43 0 04 G 28 0 25 1 04 H 28 0 25 0 04 I 28 0 25 0 04 L 28 0 25 0 04 O 28 0 25 0 04 P 28 0 25 0 04 Q 28 0 25 0 04 V 28 0 25 0 05 S 50 0 43 0 06 A 56 0 52 1 06 B 70 0 65 1 06 C 84 0 78 0 0All All 25909 0 25044 344 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 7.
Page 21 Full wwPDB EM Validation Report EMD-7577, 6CRZ
All (344) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:405:ILE:HA 1:C:409:ASN:HB2 1.74 0.701:A:1034:PHE:HB2 1:A:1045:LEU:HB2 1.77 0.671:C:444:ARG:HE 1:C:454:ASP:HB2 1.60 0.671:A:188:LYS:HB3 1:A:195:TYR:HB2 1.76 0.661:A:227:ASN:HB2 1:C:444:ARG:HH22 1.61 0.661:A:99:ARG:HH22 1:A:172:VAL:HA 1.60 0.661:B:337:VAL:HG22 1:B:387:PHE:HB2 1.78 0.651:A:334:PHE:HB2 1:A:388:VAL:HG23 1.78 0.651:B:1018:GLN:NE2 1:B:1030:HIS:O 2.29 0.651:C:285:GLU:OE1 1:C:619:TRP:NE1 2.30 0.651:C:341:GLU:HB3 1:C:386:SER:HB3 1.79 0.651:B:563:ARG:HA 1:B:570:ILE:HA 1.80 0.631:A:704:ILE:HG12 1:A:1047:VAL:HG22 1.79 0.631:B:93:GLU:HG3 1:B:183:ARG:HH21 1.64 0.631:C:366:CYS:SG 1:C:373:LYS:NZ 2.72 0.631:A:441:ARG:NH2 1:A:456:SER:O 2.32 0.621:A:99:ARG:HB3 1:A:118:ASN:HB3 1.80 0.621:A:99:ARG:HH12 1:A:172:VAL:HG12 1.65 0.621:A:126:ARG:NH2 1:A:159:CYS:SG 2.73 0.621:C:1068:LYS:HB3 1:C:1104:VAL:HG21 1.82 0.611:C:349:VAL:HG12 1:C:511:CYS:H 1.65 0.611:B:1034:PHE:HB2 1:B:1045:LEU:HB2 1.83 0.611:B:707:GLU:OE2 1:B:1010:LYS:NZ 2.33 0.611:C:355:LEU:HD22 1:C:419:CYS:HB2 1.82 0.611:C:188:LYS:HB2 1:C:195:TYR:HB2 1.81 0.611:C:325:PHE:HB3 1:C:328:VAL:HB 1.83 0.601:B:993:GLN:OE1 1:B:996:ARG:NH1 2.35 0.601:C:323:CYS:N 1:C:348:CYS:SG 2.74 0.601:A:26:GLN:HB2 1:A:75:THR:HA 1.84 0.601:A:18:ARG:HB2 1:A:151:MET:HG2 1.82 0.601:A:1036:GLN:HB2 1:A:1043:VAL:HB 1.83 0.601:B:142:LYS:HE2 1:B:240:PRO:HD3 1.83 0.601:A:541:SER:HB3 1:A:570:ILE:HG22 1.84 0.591:A:898:LEU:HD23 1:A:905:ILE:HD13 1.84 0.591:C:355:LEU:HD11 1:C:499:LEU:HD22 1.84 0.591:A:99:ARG:NH2 1:A:171:ASP:O 2.35 0.591:B:377:LEU:O 1:B:512:GLY:N 2.35 0.59
1:A:1001:ARG:NH2 1:C:999:GLU:OE2 2.36 0.591:A:415:ASP:O 1:B:965:ARG:NH2 2.36 0.59
1:B:716:THR:HG22 1:B:842:VAL:HG22 1.85 0.58Continued on next page...
Page 22 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:511:CYS:HB3 1:A:514:LYS:HD2 1.83 0.581:A:708:VAL:HG12 1:A:1043:VAL:HG22 1.86 0.581:C:716:THR:HG22 1:C:842:VAL:HG22 1.85 0.581:B:138:PHE:HB2 1:B:236:THR:HA 1.86 0.581:B:323:CYS:N 1:B:348:CYS:SG 2.77 0.581:C:70:HIS:HA 1:C:251:ALA:HA 1.85 0.58
1:B:152:ILE:HD13 1:B:234:ILE:HD13 1.85 0.581:C:186:VAL:HB 1:C:197:TYR:HB2 1.86 0.57
1:C:425:THR:HG21 1:C:495:ARG:HE 1.67 0.571:A:1086:ILE:HB 1:A:1095:GLN:HB2 1.86 0.571:B:550:GLN:OE1 1:B:563:ARG:NH2 2.37 0.571:A:1078:VAL:HG21 1:A:1087:THR:HG22 1.86 0.571:B:38:ARG:NH1 1:B:184:GLU:OE2 2.38 0.571:B:388:VAL:HG22 1:B:495:ARG:HG2 1.86 0.561:A:126:ARG:HB2 1:A:130:PHE:HZ 1.69 0.561:A:529:PHE:HB2 1:A:532:LEU:HB3 1.87 0.561:C:862:GLY:O 1:C:866:ALA:N 2.38 0.561:C:402:THR:HA 1:C:406:ALA:HB3 1.87 0.561:A:628:VAL:HG22 1:A:637:ILE:HG12 1.88 0.561:A:1038:ALA:HB2 1:A:1043:VAL:HG23 1.88 0.561:C:389:VAL:HG11 1:C:397:ILE:HD11 1.87 0.56
1:A:78:ASN:O 1:A:232:ARG:NH1 2.38 0.561:B:416:PHE:HB3 1:B:502:GLU:HB2 1.87 0.561:A:239:SER:HB3 1:A:246:GLY:H 1.70 0.561:A:354:VAL:HA 1:A:357:ASN:HB2 1.87 0.561:A:984:GLN:OE1 1:B:984:GLN:NE2 2.34 0.561:B:277:ASP:OD2 1:B:280:GLN:NE2 2.35 0.561:C:529:PHE:HB2 1:C:532:LEU:HB2 1.87 0.561:C:563:ARG:HA 1:C:570:ILE:HA 1.87 0.551:B:206:VAL:HG12 1:B:207:ARG:HG3 1.88 0.551:B:99:ARG:HH22 1:B:120:SER:HA 1.71 0.551:C:194:LEU:HD23 1:C:222:LEU:HD12 1.88 0.551:C:777:LYS:HD3 1:C:785:SER:HA 1.88 0.551:A:277:ASP:HB3 1:A:280:GLN:HG2 1.88 0.551:A:453:ARG:NH2 1:B:158:ASN:O 2.39 0.551:B:409:ASN:HD21 1:B:440:TYR:HB2 1.72 0.551:C:125:ILE:HB 1:C:163:TYR:HB3 1.89 0.551:C:92:THR:HB 1:C:251:ALA:HB3 1.88 0.551:A:824:GLY:HA3 1:A:831:LEU:HA 1.89 0.551:C:239:SER:HB3 1:C:246:GLY:H 1.71 0.551:B:383:TYR:HB2 1:B:500:SER:HB3 1.88 0.54
Continued on next page...
Page 23 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:351:ASP:HB3 1:C:513:PRO:HD3 1.88 0.541:C:96:ASN:O 1:C:99:ARG:NH1 2.41 0.541:A:404:VAL:O 1:A:409:ASN:ND2 2.41 0.54
1:A:1029:TYR:HB2 1:A:1049:TYR:HB3 1.90 0.541:C:409:ASN:HD21 1:C:440:TYR:HB2 1.72 0.541:A:381:ASN:OD1 1:A:509:THR:N 2.41 0.541:B:999:GLU:OE2 1:C:1001:ARG:NH2 2.40 0.541:A:109:ASN:O 1:A:129:ASN:ND2 2.41 0.541:B:953:GLY:O 1:B:977:ARG:NH1 2.41 0.54
1:C:745:LEU:HD22 1:C:990:VAL:HG21 1.89 0.541:A:116:ILE:HA 1:A:125:ILE:HG12 1.90 0.531:A:149:HIS:HB3 1:A:151:MET:HG3 1.90 0.531:C:340:TRP:HE1 1:C:453:ARG:HB3 1.73 0.531:C:99:ARG:HB3 1:C:118:ASN:HB3 1.90 0.531:A:383:TYR:HB2 1:A:500:SER:HB3 1.89 0.531:B:78:ASN:ND2 1:B:136:PRO:O 2.42 0.531:A:25:VAL:HG23 1:A:76:PHE:HB2 1.89 0.531:C:906:ALA:O 1:C:910:ASN:ND2 2.42 0.53
1:A:758:ARG:NH1 1:A:762:GLU:OE2 2.42 0.531:C:1029:TYR:HB2 1:C:1049:TYR:HB3 1.91 0.531:B:419:CYS:H 1:B:499:LEU:HB2 1.74 0.531:C:353:SER:HA 1:C:356:TYR:HB3 1.90 0.531:A:737:GLN:OE1 1:C:951:ASN:ND2 2.39 0.531:A:955:ILE:HG23 1:A:962:ILE:HG12 1.91 0.531:A:182:LEU:HB2 1:A:203:ILE:HD13 1.91 0.531:C:327:GLU:HG2 1:C:328:VAL:HG23 1.90 0.531:A:126:ARG:HG2 1:A:162:GLU:HG3 1.91 0.531:B:1068:LYS:HA 1:B:1107:ASN:HA 1.89 0.531:C:783:ASN:N 1:C:910:ASN:OD1 2.42 0.52
1:A:139:ALA:HB3 1:A:149:HIS:HB2 1.91 0.521:B:1063:ILE:HD11 1:B:1097:ILE:HD13 1.91 0.521:A:896:ASN:O 1:A:900:GLU:N 2.38 0.52
1:A:425:THR:OG1 1:A:493:PRO:O 2.27 0.521:A:71:THR:HB 1:A:250:ALA:HB3 1.92 0.521:A:778:TYR:HB3 4:G:1:NAG:H81 1.90 0.521:A:337:VAL:HG11 1:A:405:ILE:HD12 1.92 0.521:B:887:ARG:NH1 1:B:1031:LEU:O 2.43 0.521:C:299:ILE:HG12 1:C:584:ILE:HG12 1.90 0.521:C:373:LYS:NZ 1:C:419:CYS:SG 2.79 0.521:A:378:CYS:HA 1:A:511:CYS:HA 1.92 0.521:B:642:VAL:HB 1:B:677:TYR:HB3 1.91 0.52
Continued on next page...
Page 24 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:690:SER:OG 1:B:692:ASN:OD1 2.27 0.521:B:398:ALA:HB3 1:B:401:GLN:HG3 1.91 0.511:A:1030:HIS:NE2 1:A:1032:MET:O 2.44 0.511:B:1080:ASN:HB2 1:B:1085:PHE:HE1 1.75 0.511:B:883:GLN:HE21 1:B:887:ARG:HE 1.58 0.511:A:390:LYS:HD3 1:A:481:TYR:HB3 1.92 0.511:B:32:GLN:HG3 6:B:1301:NAG:H3 1.92 0.511:B:429:ASP:OD1 1:B:495:ARG:NH2 2.42 0.511:A:1112:ILE:HG23 6:A:1310:NAG:H62 1.93 0.511:B:99:ARG:HB2 1:B:138:PHE:HE2 1.76 0.511:A:380:SER:OG 1:A:381:ASN:N 2.44 0.511:A:297:LYS:HG3 1:A:586:PRO:HA 1.93 0.501:A:1086:ILE:HG12 1:A:1097:ILE:HG12 1.94 0.501:A:94:LYS:HB3 1:A:179:PHE:HA 1.92 0.501:B:282:PRO:HB2 1:B:594:VAL:HG21 1.92 0.501:C:930:LEU:HD21 1:C:1041:GLY:HA3 1.93 0.501:B:822:CYS:HA 1:B:833:CYS:HA 1.92 0.501:C:340:TRP:NE1 1:C:453:ARG:HB3 2.27 0.501:A:405:ILE:HA 1:A:409:ASN:HB2 1.94 0.501:B:459:PRO:HD2 1:B:469:PRO:HB2 1.94 0.501:B:762:GLU:O 1:B:766:GLN:NE2 2.39 0.501:C:62:PHE:O 1:C:620:ARG:NH2 2.45 0.50
1:A:184:GLU:HG2 1:A:216:LEU:HD21 1.94 0.501:A:366:CYS:HA 1:A:419:CYS:HA 1.93 0.501:A:818:GLN:O 1:A:838:ASN:ND2 2.44 0.50
1:A:337:VAL:HG22 1:A:387:PHE:HB2 1.92 0.491:A:711:VAL:HG12 1:A:1004:ALA:HA 1.93 0.491:A:764:PHE:HE2 1:A:852:ILE:HG23 1.78 0.491:B:405:ILE:HA 1:B:409:ASN:HB2 1.93 0.49
1:C:1057:PHE:HB3 1:C:1078:VAL:HB 1.94 0.491:A:112:GLN:HE22 1:C:453:ARG:HH21 1.60 0.491:B:316:PHE:HB3 1:B:513:PRO:HB2 1.94 0.491:A:99:ARG:NH1 1:A:147:GLN:OE1 2.46 0.491:B:422:ALA:HB1 1:B:494:TYR:HB3 1.94 0.491:C:804:LEU:HD22 1:C:927:LEU:HD11 1.94 0.491:A:609:ALA:HB1 1:A:614:GLN:HB2 1.93 0.491:B:334:PHE:HB2 1:B:388:VAL:HG23 1.94 0.491:B:389:VAL:HG11 1:B:397:ILE:HD11 1.95 0.491:A:1013:GLU:OE1 1:C:1022:VAL:N 2.46 0.491:C:886:TYR:HA 1:C:889:ASN:HD22 1.78 0.491:B:807:LYS:HD2 1:B:924:SER:HB2 1.95 0.48
Continued on next page...
Page 25 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:878:ILE:HG13 1:C:694:ILE:HG12 1.95 0.481:B:591:SER:OG 1:B:592:SER:N 2.46 0.48
1:B:958:VAL:HG12 1:B:961:ASP:H 1.77 0.481:C:1073:ARG:NH1 1:C:1100:ASP:O 2.46 0.481:C:99:ARG:HE 1:C:170:LEU:HD23 1.77 0.481:B:871:GLY:HA3 1:B:1016:LEU:HB3 1.94 0.481:C:237:ALA:HB1 1:C:245:TRP:HB3 1.95 0.481:C:94:LYS:HB3 1:C:179:PHE:HA 1.95 0.481:B:25:VAL:HG13 1:B:76:PHE:HB3 1.96 0.481:C:25:VAL:HG22 1:C:76:PHE:HD2 1.79 0.481:A:445:HIS:H 1:A:460:PHE:HZ 1.61 0.48
1:A:808:VAL:HA 1:A:931:GLN:HE21 1.79 0.481:B:194:LEU:HB3 1:B:222:LEU:HB2 1.95 0.481:B:322:LEU:HA 1:B:349:VAL:H 1.78 0.481:B:582:SER:HB2 1:B:597:LEU:HB3 1.94 0.481:C:424:ASN:ND2 1:C:492:GLN:OE1 2.46 0.481:C:394:VAL:HG21 1:C:494:TYR:HD2 1.78 0.481:C:332:THR:O 1:C:495:ARG:NH1 2.47 0.481:A:1029:TYR:O 1:A:1049:TYR:N 2.44 0.481:C:586:PRO:HD3 1:C:674:ILE:HD11 1.96 0.481:A:48:ARG:HB2 1:A:266:TYR:CD2 2.49 0.471:C:422:ALA:HB1 1:C:494:TYR:HB3 1.95 0.471:C:848:THR:H 1:C:851:MET:HE3 1.79 0.47
1:C:429:ASP:OD2 1:C:495:ARG:NH2 2.47 0.471:A:804:LEU:HD13 1:A:1043:VAL:HG21 1.96 0.471:A:1070:TYR:HD2 1:A:1119:VAL:HG21 1.78 0.471:B:116:ILE:HG12 1:B:125:ILE:HG12 1.95 0.471:C:344:LYS:HA 1:C:383:TYR:HA 1.97 0.47
1:A:441:ARG:HH22 1:A:456:SER:HB3 1.80 0.471:C:182:LEU:HD22 1:C:203:ILE:HD12 1.96 0.471:C:196:VAL:HB 1:C:220:PHE:H 1.80 0.47
1:C:1062:ALA:HB3 1:C:1114:ILE:HG12 1.97 0.471:C:1111:VAL:HB 1:C:1114:ILE:HD11 1.97 0.471:C:804:LEU:HD21 1:C:920:LEU:HD13 1.95 0.471:B:331:ALA:HB3 1:B:334:PHE:HE1 1.79 0.471:C:126:ARG:HG2 1:C:162:GLU:HG3 1.97 0.471:A:1000:ILE:O 1:A:1004:ALA:N 2.47 0.46
1:A:708:VAL:HG23 1:A:929:LYS:HD2 1.97 0.461:C:102:VAL:HG23 1:C:115:ILE:HG12 1.97 0.461:A:175:LYS:HZ2 1:A:180:LYS:HD2 1.80 0.461:B:38:ARG:NH2 1:B:210:PRO:O 2.47 0.46
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Page 26 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:361:PHE:HA 1:A:423:TRP:HB2 1.97 0.461:A:711:VAL:HG22 1:A:1041:GLY:HA2 1.97 0.461:B:429:ASP:O 1:B:435:ASN:ND2 2.38 0.461:C:1062:ALA:O 1:C:1115:ILE:N 2.38 0.461:B:348:CYS:SG 1:B:349:VAL:N 2.89 0.461:C:712:SER:OG 1:C:713:MET:N 2.49 0.461:A:878:ILE:HG23 1:A:883:GLN:HE21 1.80 0.461:B:23:ASP:HB3 1:B:244:ILE:HG23 1.97 0.46
1:A:389:VAL:HG11 1:A:397:ILE:HD11 1.99 0.451:A:405:ILE:HD13 1:A:409:ASN:HD22 1.81 0.451:C:99:ARG:CZ 1:C:172:VAL:HG12 2.45 0.45
1:B:328:VAL:HG13 1:B:343:LYS:HD2 1.98 0.451:B:326:GLY:HA2 1:B:330:ASN:HB3 1.99 0.451:A:835:GLN:NE2 1:C:600:ASP:O 2.48 0.451:A:48:ARG:HB2 1:A:266:TYR:HD2 1.80 0.451:A:1018:GLN:NE2 1:A:1030:HIS:O 2.44 0.451:C:537:VAL:HB 1:C:574:SER:HB3 1.97 0.451:B:405:ILE:HG12 1:B:409:ASN:HD22 1.82 0.451:C:598:TYR:HB2 1:C:635:CYS:HB2 1.98 0.451:A:102:VAL:HB 1:A:232:ARG:HB3 1.99 0.451:A:365:LYS:NZ 1:A:366:CYS:O 2.49 0.451:B:188:LYS:HE3 1:B:195:TYR:HD2 1.82 0.45
1:A:363:THR:HG21 1:A:422:ALA:HB3 1.99 0.441:B:337:VAL:HG12 1:B:409:ASN:HB3 2.00 0.441:A:897:VAL:HA 1:A:900:GLU:HB2 1.99 0.44
1:A:109:ASN:HD22 1:A:131:GLU:HG2 1.82 0.441:A:585:THR:HB 1:A:594:VAL:HG12 1.98 0.441:C:425:THR:HB 1:C:428:ILE:HB 1.98 0.441:A:917:GLN:O 1:A:921:THR:OG1 2.27 0.44
1:C:871:GLY:HA2 1:C:1016:LEU:HD22 1.98 0.441:A:31:THR:O 1:A:68:GLY:N 2.42 0.44
1:B:114:VAL:HG11 1:B:224:LEU:HD13 1.98 0.441:A:582:SER:HB2 1:A:597:LEU:HB3 2.00 0.441:B:1057:PHE:HB3 1:B:1078:VAL:HG13 2.00 0.441:C:310:SER:N 1:C:524:CYS:O 2.50 0.441:A:591:SER:OG 1:A:592:SER:N 2.50 0.441:B:521:LYS:HD3 1:B:540:PRO:HD3 1.99 0.441:A:959:LEU:HD23 1:A:962:ILE:HD12 2.00 0.441:B:1063:ILE:HG23 1:B:1117:ASN:HB3 2.00 0.441:C:808:VAL:HG12 1:C:809:THR:HG23 2.00 0.441:B:352:TYR:HB3 1:B:355:LEU:HB2 1.99 0.43
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Page 27 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:766:GLN:NE2 1:C:1012:SER:OG 2.45 0.431:C:92:THR:N 1:C:251:ALA:O 2.47 0.43
1:A:745:LEU:HD22 1:A:990:VAL:HG21 2.00 0.431:A:81:ILE:HG21 1:A:254:VAL:HG21 1.98 0.431:A:98:VAL:O 1:A:183:ARG:NH2 2.46 0.43
1:C:1071:PHE:HZ 1:C:1111:VAL:HG21 1.83 0.431:C:564:ASP:OD2 1:C:567:THR:OG1 2.25 0.431:A:1108:CYS:SG 1:A:1109:ASP:N 2.91 0.431:A:451:PHE:HD2 1:B:192:GLY:HA3 1.82 0.431:C:685:SER:OG 1:C:686:SER:N 2.51 0.431:B:584:ILE:HB 1:B:595:ALA:HB3 1.99 0.431:C:1012:SER:HA 1:C:1016:LEU:HD12 2.01 0.431:C:390:LYS:HE2 1:C:481:TYR:HD1 1.83 0.431:A:444:ARG:NH1 1:A:454:ASP:OD2 2.52 0.431:A:238:PHE:H 1:A:247:THR:HA 1.83 0.43
1:B:324:PRO:HD2 1:B:345:ILE:HG23 2.01 0.431:A:1063:ILE:HG12 1:A:1117:ASN:HD22 1.83 0.43
1:B:31:THR:O 1:B:68:GLY:N 2.50 0.431:B:822:CYS:HB3 1:B:833:CYS:HB2 1.91 0.431:B:82:PRO:HB3 1:B:84:LYS:HE3 2.00 0.431:B:182:LEU:HB2 1:B:203:ILE:HD13 1.99 0.431:A:420:VAL:HG22 1:A:498:VAL:HG22 2.00 0.431:A:694:ILE:HG22 1:A:1059:THR:HB 2.01 0.431:B:179:PHE:HB2 1:B:205:VAL:HB 2.00 0.421:B:277:ASP:HB3 1:B:280:GLN:HG2 2.01 0.421:B:186:VAL:HG13 1:B:257:LEU:HD11 2.02 0.421:A:21:THR:HG22 1:A:135:ASN:H 1.84 0.421:A:152:ILE:HD13 1:A:234:ILE:HD13 2.02 0.421:A:96:ASN:O 1:A:99:ARG:NE 2.51 0.421:B:955:ILE:HB 1:B:974:GLN:HE22 1.83 0.42
1:C:704:ILE:HG12 1:C:1047:VAL:HG22 2.02 0.421:A:127:ALA:HB3 1:A:161:PHE:H 1.84 0.421:A:787:ILE:HD11 1:A:913:ILE:HD12 2.01 0.421:B:104:GLY:HA2 1:B:226:ILE:HD12 2.01 0.421:B:203:ILE:HB 1:B:205:VAL:HG23 2.01 0.42
1:B:282:PRO:HG3 1:B:619:TRP:CE2 2.55 0.421:B:758:ARG:O 1:B:762:GLU:N 2.45 0.42
1:C:1052:SER:OG 1:C:1053:GLN:N 2.52 0.421:B:248:SER:OG 1:B:249:ALA:N 2.52 0.421:A:209:LEU:HB2 1:A:253:PHE:CZ 2.55 0.421:B:1029:TYR:HB2 1:B:1049:TYR:HB3 2.00 0.42
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:B:286:LEU:HD11 1:B:300:TYR:HB2 2.01 0.421:B:429:ASP:OD2 1:B:495:ARG:NE 2.49 0.421:C:83:PHE:HE2 1:C:189:ASN:HB2 1.84 0.421:C:26:GLN:HB2 1:C:75:THR:HA 2.02 0.421:B:285:GLU:OE1 1:B:619:TRP:NE1 2.52 0.421:C:248:SER:OG 1:C:249:ALA:N 2.51 0.421:B:697:PRO:O 1:B:1092:PHE:N 2.53 0.421:C:329:PHE:HA 1:C:497:VAL:HG21 2.01 0.421:C:365:LYS:HB2 1:C:420:VAL:HB 2.02 0.421:B:1079:PHE:HB2 1:B:1084:TRP:CH2 2.54 0.421:B:923:THR:OG1 1:B:924:SER:N 2.51 0.421:A:407:ASP:OD2 1:A:447:LYS:NZ 2.39 0.411:B:197:TYR:CD1 1:B:218:PRO:HA 2.55 0.411:B:710:PRO:HA 1:B:1041:GLY:HA3 2.03 0.41
1:A:1054:GLU:HG2 1:B:876:LEU:HD21 2.01 0.411:C:887:ARG:NH1 1:C:1031:LEU:O 2.51 0.411:C:377:LEU:HB3 1:C:501:PHE:HZ 1.85 0.411:A:444:ARG:HH22 1:A:448:LEU:HG 1.84 0.411:B:631:THR:OG1 1:B:634:GLY:N 2.49 0.411:C:116:ILE:HG12 1:C:125:ILE:HG12 2.02 0.411:C:600:ASP:N 1:C:633:ALA:O 2.44 0.41
1:B:1080:ASN:HB3 1:B:1083:SER:H 1.86 0.411:C:1079:PHE:HB2 1:C:1084:TRP:CD2 2.55 0.411:A:83:PHE:CZ 1:A:86:GLY:HA2 2.56 0.411:A:305:PHE:HZ 1:A:601:VAL:HG11 1.85 0.411:A:96:ASN:HB2 1:A:99:ARG:HH21 1.86 0.411:C:545:PHE:HB2 1:C:563:ARG:HH21 1.86 0.411:B:663:VAL:H 1:B:672:LYS:N 2.19 0.41
1:C:182:LEU:HD23 1:C:201:GLN:HE21 1.86 0.411:C:546:GLN:H 1:C:549:GLN:HB2 1.86 0.411:A:39:GLY:HA3 1:A:60:LEU:HB3 2.02 0.411:B:1080:ASN:HB3 1:B:1082:THR:H 1.86 0.411:B:888:PHE:HE2 1:B:898:LEU:HD13 1.86 0.411:A:1071:PHE:HZ 1:A:1111:VAL:HG21 1.85 0.411:A:372:THR:HG21 1:B:968:PRO:HD3 2.02 0.411:C:99:ARG:HH21 1:C:170:LEU:HG 1.85 0.411:B:683:ALA:HB3 1:C:769:GLN:HG2 2.03 0.41
1:A:1111:VAL:HG13 1:B:899:TYR:HB3 2.02 0.411:A:735:LEU:HA 1:A:738:TYR:HD2 1.86 0.411:A:112:GLN:NE2 1:C:453:ARG:HH21 2.19 0.411:C:893:VAL:HA 1:C:1091:PHE:HE1 1.86 0.41
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:102:VAL:N 1:A:232:ARG:O 2.42 0.401:B:788:LEU:HD23 1:B:788:LEU:HA 1.82 0.401:C:363:THR:HG21 1:C:394:VAL:HG11 2.03 0.401:C:649:ASP:HB3 1:C:659:SER:HB2 2.03 0.401:C:313:VAL:HG11 1:C:519:LEU:HD12 2.03 0.401:B:76:PHE:CZ 1:B:235:LEU:HB2 2.56 0.40
1:A:306:ARG:NH2 1:B:727:ASP:OD1 2.43 0.401:B:632:GLN:HE21 1:C:825:ASP:HA 1.86 0.401:A:373:LYS:HE2 1:B:965:ARG:HG2 2.04 0.40
1:C:1059:THR:HG22 1:C:1078:VAL:HG12 2.02 0.401:C:21:THR:HB 1:C:135:ASN:HB2 2.04 0.401:C:25:VAL:HA 1:C:76:PHE:HB3 2.02 0.401:C:48:ARG:HB2 1:C:266:TYR:CD2 2.57 0.401:C:469:PRO:HA 1:C:471:ALA:H 1.87 0.401:A:530:ASN:H 1:A:565:PRO:HG2 1.87 0.401:B:405:ILE:O 1:B:410:TYR:N 2.40 0.40
1:C:1060:ALA:HA 1:C:1061:PRO:HD3 1.93 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 1054/1215 (87%) 962 (91%) 92 (9%) 0 100 100
1 B 1054/1215 (87%) 973 (92%) 81 (8%) 0 100 100
1 C 1055/1215 (87%) 982 (93%) 73 (7%) 0 100 100
All All 3163/3645 (87%) 2917 (92%) 246 (8%) 0 100 100
There are no Ramachandran outliers to report.
Page 30 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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 926/1053 (88%) 926 (100%) 0 100 100
1 B 927/1053 (88%) 926 (100%) 1 (0%) 93 97
1 C 927/1053 (88%) 927 (100%) 0 100 100
All All 2780/3159 (88%) 2779 (100%) 1 (0%) 100 100
All (1) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type1 B 589 ASN
Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (17)such sidechains are listed below:
Mol Chain Res Type1 A 112 GLN1 A 230 ASN1 A 733 ASN1 A 883 GLN1 A 908 GLN1 A 931 GLN1 A 1117 ASN1 B 112 GLN1 B 733 ASN1 B 806 ASN1 B 883 GLN1 B 896 ASN1 C 112 GLN1 C 201 GLN1 C 347 ASN1 C 889 ASN1 C 908 GLN
Page 31 Full wwPDB EM Validation Report EMD-7577, 6CRZ
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○
51 monosaccharides 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
2 NAG D 1 1,2 14,14,15 0.40 0 17,19,21 0.59 02 NAG D 2 2 14,14,15 0.30 0 17,19,21 1.08 1 (5%)2 BMA D 3 2 11,11,12 0.94 0 15,15,17 0.80 03 NAG E 1 1,3 14,14,15 0.40 0 17,19,21 0.63 03 NAG E 2 3 14,14,15 0.29 0 17,19,21 0.49 03 BMA E 3 3 11,11,12 0.63 0 15,15,17 0.89 03 MAN E 4 3 11,11,12 0.81 0 15,15,17 1.07 2 (13%)2 NAG F 1 1,2 14,14,15 0.54 0 17,19,21 0.65 02 NAG F 2 2 14,14,15 0.37 0 17,19,21 0.46 02 BMA F 3 2 11,11,12 0.66 0 15,15,17 1.01 1 (6%)4 NAG G 1 1,4 14,14,15 0.45 0 17,19,21 0.56 04 NAG G 2 4 14,14,15 0.22 0 17,19,21 0.51 04 NAG H 1 1,4 14,14,15 0.41 0 17,19,21 0.64 04 NAG H 2 4 14,14,15 0.26 0 17,19,21 0.56 04 NAG I 1 1,4 14,14,15 0.72 1 (7%) 17,19,21 0.63 04 NAG I 2 4 14,14,15 0.46 0 17,19,21 0.48 02 NAG J 1 1,2 14,14,15 0.30 0 17,19,21 0.45 02 NAG J 2 2 14,14,15 0.30 0 17,19,21 0.49 02 BMA J 3 2 11,11,12 0.88 0 15,15,17 0.82 02 NAG K 1 1,2 14,14,15 0.35 0 17,19,21 0.62 1 (5%)2 NAG K 2 2 14,14,15 0.31 0 17,19,21 0.50 0
Page 32 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2
2 BMA K 3 2 11,11,12 0.82 0 15,15,17 0.80 04 NAG L 1 1,4 14,14,15 0.29 0 17,19,21 0.37 04 NAG L 2 4 14,14,15 0.22 0 17,19,21 0.64 1 (5%)2 NAG M 1 1,2 14,14,15 0.30 0 17,19,21 0.56 02 NAG M 2 2 14,14,15 0.43 0 17,19,21 0.63 02 BMA M 3 2 11,11,12 0.77 0 15,15,17 0.85 02 NAG N 1 1,2 14,14,15 0.36 0 17,19,21 0.53 02 NAG N 2 2 14,14,15 0.22 0 17,19,21 0.69 1 (5%)2 BMA N 3 2 11,11,12 0.86 0 15,15,17 0.78 04 NAG O 1 1,4 14,14,15 0.41 0 17,19,21 0.78 1 (5%)4 NAG O 2 4 14,14,15 0.60 0 17,19,21 0.38 04 NAG P 1 1,4 14,14,15 0.28 0 17,19,21 0.49 04 NAG P 2 4 14,14,15 0.29 0 17,19,21 0.42 04 NAG Q 1 1,4 14,14,15 0.31 0 17,19,21 0.50 04 NAG Q 2 4 14,14,15 0.34 0 17,19,21 0.42 02 NAG R 1 1,2 14,14,15 0.21 0 17,19,21 0.98 1 (5%)2 NAG R 2 2 14,14,15 0.20 0 17,19,21 0.58 02 BMA R 3 2 11,11,12 0.74 0 15,15,17 0.95 1 (6%)5 NAG S 1 1,5 14,14,15 0.36 0 17,19,21 0.42 05 NAG S 2 5 14,14,15 0.26 0 17,19,21 0.55 05 BMA S 3 5 11,11,12 0.85 0 15,15,17 1.36 1 (6%)5 MAN S 4 5 11,11,12 1.01 1 (9%) 15,15,17 1.30 2 (13%)2 NAG T 1 1,2 14,14,15 0.63 1 (7%) 17,19,21 0.59 02 NAG T 2 2 14,14,15 0.31 0 17,19,21 0.70 02 BMA T 3 2 11,11,12 0.65 0 15,15,17 1.05 1 (6%)2 NAG U 1 1,2 14,14,15 0.45 0 17,19,21 0.46 02 NAG U 2 2 14,14,15 0.34 0 17,19,21 0.62 1 (5%)2 BMA U 3 2 11,11,12 0.76 0 15,15,17 0.85 04 NAG V 1 1,4 14,14,15 0.26 0 17,19,21 0.39 04 NAG V 2 4 14,14,15 0.26 0 17,19,21 0.50 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 Rings2 NAG D 1 1,2 - 2/6/23/26 0/1/1/12 NAG D 2 2 - 2/6/23/26 0/1/1/12 BMA D 3 2 - 0/2/19/22 0/1/1/1
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Continued from previous page...Mol Type Chain Res Link Chirals Torsions Rings3 NAG E 1 1,3 - 2/6/23/26 0/1/1/13 NAG E 2 3 - 1/6/23/26 0/1/1/13 BMA E 3 3 - 2/2/19/22 0/1/1/13 MAN E 4 3 - 2/2/19/22 0/1/1/12 NAG F 1 1,2 - 2/6/23/26 0/1/1/12 NAG F 2 2 - 2/6/23/26 0/1/1/12 BMA F 3 2 - 0/2/19/22 0/1/1/14 NAG G 1 1,4 - 2/6/23/26 0/1/1/14 NAG G 2 4 - 2/6/23/26 0/1/1/14 NAG H 1 1,4 - 0/6/23/26 0/1/1/14 NAG H 2 4 - 0/6/23/26 0/1/1/14 NAG I 1 1,4 - 1/6/23/26 0/1/1/14 NAG I 2 4 - 2/6/23/26 0/1/1/12 NAG J 1 1,2 - 1/6/23/26 0/1/1/12 NAG J 2 2 - 0/6/23/26 0/1/1/12 BMA J 3 2 - 2/2/19/22 0/1/1/12 NAG K 1 1,2 - 0/6/23/26 0/1/1/12 NAG K 2 2 - 2/6/23/26 0/1/1/12 BMA K 3 2 - 2/2/19/22 0/1/1/14 NAG L 1 1,4 - 1/6/23/26 0/1/1/14 NAG L 2 4 - 2/6/23/26 0/1/1/12 NAG M 1 1,2 - 2/6/23/26 0/1/1/12 NAG M 2 2 - 2/6/23/26 0/1/1/12 BMA M 3 2 - 2/2/19/22 0/1/1/12 NAG N 1 1,2 - 2/6/23/26 0/1/1/12 NAG N 2 2 - 0/6/23/26 0/1/1/12 BMA N 3 2 - 2/2/19/22 0/1/1/14 NAG O 1 1,4 - 2/6/23/26 0/1/1/14 NAG O 2 4 - 0/6/23/26 0/1/1/14 NAG P 1 1,4 - 2/6/23/26 0/1/1/14 NAG P 2 4 - 2/6/23/26 0/1/1/14 NAG Q 1 1,4 - 2/6/23/26 0/1/1/14 NAG Q 2 4 - 2/6/23/26 0/1/1/12 NAG R 1 1,2 - 1/6/23/26 0/1/1/12 NAG R 2 2 - 2/6/23/26 0/1/1/12 BMA R 3 2 - 2/2/19/22 0/1/1/1
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Page 34 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...Mol Type Chain Res Link Chirals Torsions Rings5 NAG S 1 1,5 - 2/6/23/26 0/1/1/15 NAG S 2 5 - 2/6/23/26 0/1/1/15 BMA S 3 5 - 1/2/19/22 0/1/1/15 MAN S 4 5 - 0/2/19/22 0/1/1/12 NAG T 1 1,2 - 0/6/23/26 0/1/1/12 NAG T 2 2 - 2/6/23/26 0/1/1/12 BMA T 3 2 - 2/2/19/22 0/1/1/12 NAG U 1 1,2 - 0/6/23/26 0/1/1/12 NAG U 2 2 - 1/6/23/26 0/1/1/12 BMA U 3 2 - 0/2/19/22 0/1/1/14 NAG V 1 1,4 - 2/6/23/26 0/1/1/14 NAG V 2 4 - 0/6/23/26 0/1/1/1
All (3) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)5 S 4 MAN C1-C2 2.63 1.58 1.522 T 1 NAG O5-C1 -2.08 1.40 1.434 I 1 NAG O5-C1 2.06 1.47 1.43
All (15) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 S 3 BMA C1-O5-C5 3.79 117.33 112.192 D 2 NAG C1-O5-C5 3.50 116.94 112.192 R 1 NAG C1-O5-C5 3.22 116.55 112.195 S 4 MAN C1-O5-C5 2.94 116.17 112.192 F 3 BMA C1-O5-C5 2.85 116.06 112.193 E 4 MAN C1-O5-C5 2.53 115.62 112.194 O 1 NAG C1-O5-C5 2.51 115.59 112.192 T 3 BMA C1-O5-C5 2.47 115.54 112.192 R 3 BMA C1-O5-C5 2.45 115.51 112.192 N 2 NAG C1-O5-C5 2.39 115.43 112.194 L 2 NAG C1-O5-C5 2.31 115.33 112.195 S 4 MAN O2-C2-C3 -2.18 105.78 110.143 E 4 MAN O2-C2-C3 -2.16 105.81 110.142 U 2 NAG C1-O5-C5 2.08 115.02 112.192 K 1 NAG C1-O5-C5 2.01 114.92 112.19
There are no chirality outliers.
Page 35 Full wwPDB EM Validation Report EMD-7577, 6CRZ
All (69) torsion outliers are listed below:
Mol Chain Res Type Atoms2 K 2 NAG O5-C5-C6-O62 N 3 BMA C4-C5-C6-O62 D 1 NAG O5-C5-C6-O64 O 1 NAG O5-C5-C6-O62 K 3 BMA O5-C5-C6-O64 P 2 NAG O5-C5-C6-O63 E 1 NAG O5-C5-C6-O64 O 1 NAG C4-C5-C6-O62 N 3 BMA O5-C5-C6-O62 R 3 BMA O5-C5-C6-O64 L 2 NAG O5-C5-C6-O64 G 1 NAG O5-C5-C6-O62 M 1 NAG O5-C5-C6-O62 T 2 NAG O5-C5-C6-O62 K 2 NAG C4-C5-C6-O62 N 1 NAG C4-C5-C6-O65 S 1 NAG O5-C5-C6-O62 N 1 NAG O5-C5-C6-O62 F 1 NAG O5-C5-C6-O62 D 1 NAG C4-C5-C6-O62 T 3 BMA O5-C5-C6-O62 F 2 NAG C4-C5-C6-O62 K 3 BMA C4-C5-C6-O64 P 2 NAG C4-C5-C6-O62 T 2 NAG C4-C5-C6-O65 S 1 NAG C4-C5-C6-O62 F 1 NAG C4-C5-C6-O63 E 1 NAG C4-C5-C6-O62 R 2 NAG O5-C5-C6-O65 S 2 NAG O5-C5-C6-O64 I 2 NAG O5-C5-C6-O62 M 1 NAG C4-C5-C6-O62 J 3 BMA C4-C5-C6-O62 R 3 BMA C4-C5-C6-O63 E 4 MAN O5-C5-C6-O64 G 2 NAG O5-C5-C6-O62 D 2 NAG O5-C5-C6-O64 L 2 NAG C4-C5-C6-O62 R 2 NAG C4-C5-C6-O62 M 3 BMA O5-C5-C6-O64 P 1 NAG O5-C5-C6-O64 G 2 NAG C4-C5-C6-O6
Continued on next page...
Page 36 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...Mol Chain Res Type Atoms3 E 4 MAN C4-C5-C6-O62 D 2 NAG C4-C5-C6-O62 F 2 NAG O5-C5-C6-O64 Q 1 NAG C4-C5-C6-O64 G 1 NAG C4-C5-C6-O63 E 3 BMA O5-C5-C6-O65 S 2 NAG C4-C5-C6-O64 I 1 NAG O5-C5-C6-O64 I 2 NAG C4-C5-C6-O62 J 3 BMA O5-C5-C6-O63 E 3 BMA C4-C5-C6-O64 V 1 NAG C4-C5-C6-O62 R 1 NAG O5-C5-C6-O62 U 2 NAG O5-C5-C6-O62 M 2 NAG C4-C5-C6-O64 Q 1 NAG O5-C5-C6-O62 M 3 BMA C4-C5-C6-O62 M 2 NAG O5-C5-C6-O64 L 1 NAG O5-C5-C6-O64 V 1 NAG O5-C5-C6-O64 Q 2 NAG C4-C5-C6-O64 Q 2 NAG O5-C5-C6-O65 S 3 BMA O5-C5-C6-O62 J 1 NAG C4-C5-C6-O62 T 3 BMA C4-C5-C6-O63 E 2 NAG O5-C5-C6-O64 P 1 NAG C4-C5-C6-O6
There are no ring outliers.
1 monomer is involved in 1 short contact:
Mol Chain Res Type Clashes Symm-Clashes4 G 1 NAG 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 oligosaccharide.
Page 37 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain D
Bond lengths Bond angles
Torsions Rings
Oligosaccharide Chain F
Bond lengths Bond angles
Torsions Rings
Page 38 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain J
Bond lengths Bond angles
Torsions Rings
Oligosaccharide Chain K
Bond lengths Bond angles
Torsions Rings
Page 39 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain M
Bond lengths Bond angles
Torsions Rings
Oligosaccharide Chain N
Bond lengths Bond angles
Torsions Rings
Page 40 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain R
Bond lengths Bond angles
Torsions Rings
Oligosaccharide Chain T
Bond lengths Bond angles
Torsions Rings
Page 41 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain U
Bond lengths Bond angles
Torsions Rings
Oligosaccharide Chain E
Bond lengths Bond angles
Torsions Rings
Page 42 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain G
Bond lengths Bond angles
Torsions Rings
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Oligosaccharide Chain H
Bond lengths Bond angles
Torsions Rings
Page 44 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain I
Bond lengths Bond angles
Torsions Rings
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Oligosaccharide Chain L
Bond lengths Bond angles
Torsions Rings
Page 46 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain O
Bond lengths Bond angles
Torsions Rings
Page 47 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain P
Bond lengths Bond angles
Torsions Rings
Page 48 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain Q
Bond lengths Bond angles
Torsions Rings
Page 49 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain V
Bond lengths Bond angles
Torsions Rings
Page 50 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Oligosaccharide Chain S
Bond lengths Bond angles
Torsions Rings
5.6 Ligand geometry i○
15 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
6 NAG A 1310 1 14,14,15 0.22 0 17,19,21 0.63 1 (5%)6 NAG C 1304 1 14,14,15 0.45 0 17,19,21 0.71 1 (5%)6 NAG C 1308 1 14,14,15 0.26 0 17,19,21 0.65 1 (5%)6 NAG A 1301 1 14,14,15 0.39 0 17,19,21 0.73 1 (5%)6 NAG B 1321 1 14,14,15 0.26 0 17,19,21 0.43 06 NAG A 1305 1 14,14,15 0.42 0 17,19,21 0.52 06 NAG A 1316 1 14,14,15 0.45 0 17,19,21 0.66 1 (5%)6 NAG B 1311 1 14,14,15 0.40 0 17,19,21 0.41 0
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Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2
6 NAG C 1320 1 14,14,15 0.45 0 17,19,21 0.61 1 (5%)6 NAG B 1308 1 14,14,15 0.31 0 17,19,21 0.47 06 NAG C 1301 1 14,14,15 0.36 0 17,19,21 0.62 1 (5%)6 NAG B 1320 1 14,14,15 0.27 0 17,19,21 0.64 1 (5%)6 NAG B 1301 1 14,14,15 0.28 0 17,19,21 0.40 06 NAG C 1312 1 14,14,15 0.34 0 17,19,21 0.55 06 NAG C 1307 1 14,14,15 0.31 0 17,19,21 0.32 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 Rings6 NAG A 1310 1 - 2/6/23/26 0/1/1/16 NAG C 1304 1 - 0/6/23/26 0/1/1/16 NAG C 1308 1 - 2/6/23/26 0/1/1/16 NAG A 1301 1 - 2/6/23/26 0/1/1/16 NAG B 1321 1 - 0/6/23/26 0/1/1/16 NAG A 1305 1 - 2/6/23/26 0/1/1/16 NAG A 1316 1 - 2/6/23/26 0/1/1/16 NAG B 1311 1 - 2/6/23/26 0/1/1/16 NAG C 1320 1 - 0/6/23/26 0/1/1/16 NAG B 1308 1 - 1/6/23/26 0/1/1/16 NAG C 1301 1 - 2/6/23/26 0/1/1/16 NAG B 1320 1 - 2/6/23/26 0/1/1/16 NAG B 1301 1 - 2/6/23/26 0/1/1/16 NAG C 1312 1 - 0/6/23/26 0/1/1/16 NAG C 1307 1 - 1/6/23/26 0/1/1/1
There are no bond length outliers.
All (8) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)6 A 1301 NAG C1-O5-C5 2.55 115.65 112.196 C 1304 NAG C1-O5-C5 2.55 115.65 112.196 B 1320 NAG C1-O5-C5 2.35 115.37 112.196 A 1316 NAG C1-O5-C5 2.32 115.34 112.196 C 1308 NAG C1-O5-C5 2.29 115.30 112.19
Continued on next page...
Page 52 Full wwPDB EM Validation Report EMD-7577, 6CRZ
Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)6 A 1310 NAG C1-O5-C5 2.15 115.11 112.196 C 1301 NAG C1-O5-C5 2.12 115.06 112.196 C 1320 NAG C1-O5-C5 2.09 115.03 112.19
There are no chirality outliers.
All (20) torsion outliers are listed below:
Mol Chain Res Type Atoms6 A 1316 NAG O5-C5-C6-O66 A 1301 NAG O5-C5-C6-O66 B 1320 NAG O5-C5-C6-O66 A 1316 NAG C4-C5-C6-O66 A 1305 NAG O5-C5-C6-O66 A 1301 NAG C4-C5-C6-O66 B 1311 NAG C4-C5-C6-O66 B 1301 NAG O5-C5-C6-O66 B 1311 NAG O5-C5-C6-O66 A 1310 NAG O5-C5-C6-O66 B 1320 NAG C4-C5-C6-O66 B 1301 NAG C4-C5-C6-O66 A 1310 NAG C4-C5-C6-O66 C 1308 NAG O5-C5-C6-O66 C 1301 NAG O5-C5-C6-O66 C 1308 NAG C4-C5-C6-O66 C 1301 NAG C4-C5-C6-O66 B 1308 NAG O5-C5-C6-O66 A 1305 NAG C4-C5-C6-O66 C 1307 NAG O5-C5-C6-O6
There are no ring outliers.
2 monomers are involved in 2 short contacts:
Mol Chain Res Type Clashes Symm-Clashes6 A 1310 NAG 1 06 B 1301 NAG 1 0
5.7 Other polymers i○
There are no such residues in this entry.
Page 53 Full wwPDB EM Validation Report EMD-7577, 6CRZ
5.8 Polymer linkage issues i○
There are no chain breaks in this entry.
Page 54 Full wwPDB EM Validation Report EMD-7577, 6CRZ
6 Map visualisation i○
This section contains visualisations of the EMDB entry EMD-7577. These allow visual inspectionof the internal detail of the map and identification of artifacts.
Images derived from a raw map, generated by summing the deposited half-maps, are presentedbelow the corresponding image components of the primary map to allow further visual inspectionand comparison with those of the primary map.
6.1 Orthogonal projections i○
6.1.1 Primary map
X Y Z
6.1.2 Raw map
X Y Z
The images above show the map projected in three orthogonal directions.
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6.2 Central slices i○
6.2.1 Primary map
X Index: 160 Y Index: 160 Z Index: 160
6.2.2 Raw map
X Index: 160 Y Index: 160 Z Index: 160
The images above show central slices of the map in three orthogonal directions.
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6.3 Largest variance slices i○
6.3.1 Primary map
X Index: 154 Y Index: 155 Z Index: 148
6.3.2 Raw map
X Index: 171 Y Index: 158 Z Index: 144
The images above show the largest variance slices of the map in three orthogonal directions.
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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 0.069.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.
6.4.2 Raw map
X Y Z
These images show the 3D surface of the raw map. The raw map’s contour level was selected sothat its surface encloses the same volume as the primary map does at its recommended contourlevel.
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6.5 Mask visualisation i○
This section shows the 3D surface view of the primary map at 50% transparency overlaid with thespecified mask at 0% transparency
A mask typically either:
• Encompasses the whole structure
• Separates out a domain, a functional unit, a monomer or an area of interest from a largerstructure
6.5.1 emd_7577_msk_1.map i○
X Y Z
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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.
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7.2 Volume estimate i○
The volume at the recommended contour level is 76 nm3; this corresponds to an approximate massof 69 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.
Page 61 Full wwPDB EM Validation Report EMD-7577, 6CRZ
7.3 Rotationally averaged power spectrum i○
*Reported resolution corresponds to spatial frequency of 0.303 Å−1
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8 Fourier-Shell correlation i○
Fourier-Shell Correlation (FSC) is the most commonly used method to estimate the resolution ofsingle-particle and subtomogram-averaged maps. The shape of the curve depends on the imposedsymmetry, mask and whether or not the two 3D reconstructions used were processed from acommon reference. The reported resolution is shown as a black line. A curve is displayed for thehalf-bit criterion in addition to lines showing the 0.143 gold standard cut-off and 0.5 cut-off.
8.1 FSC i○
*Reported resolution corresponds to spatial frequency of 0.303 Å−1
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8.2 Resolution estimates i○
Resolution estimate (Å) Estimation criterion (FSC cut-off)0.143 0.5 Half-bit
Reported by author 3.30 - -Author-provided FSC curve 3.36 3.74 3.38
Calculated* 3.72 4.24 3.80
*Resolution estimate based on FSC curve calculated by comparison of deposited half-maps. Thevalue from deposited half-maps intersecting FSC 0.143 CUT-OFF 3.72 differs from the reportedvalue 3.3 by more than 10 %
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9 Map-model fit i○
This section contains information regarding the fit between EMDB map EMD-7577 and PDBmodel 6CRZ. Per-residue inclusion information can be found in section 3 on page 9.
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 0.069at 50% 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.
Page 65 Full wwPDB EM Validation Report EMD-7577, 6CRZ
9.2 Atom inclusion i○
At the recommended contour level, 20% of all backbone atoms, 15% of all non-hydrogen atoms,are inside the map.