Full wwPDB/EMDataBank EM Map/Model Validation Report...
Transcript of Full wwPDB/EMDataBank EM Map/Model Validation Report...
Full wwPDB EM Map/Model Validation Report iO
Aug 22, 2020 � 04:38 PM BST
PDB ID : 6CGREMDB ID : EMD-7472
Title : CryoEM structure of herpes simplex virus 1 capsid with associated tegumentprotein complexes.
Authors : Dai, X.H.; Zhou, Z.H.Deposited on : 2018-02-20Resolution : 4.20 Å(reported)
This is a Full wwPDB EM Map/Model 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 speci�c help available everywhere you see the iO symbol.
The following versions of software and data (see references iO) were used in the production of this report:
EMDB validation analysis : 0.0.0.dev33MolProbity : 4.02b-467
Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Ideal geometry (proteins) : Engh & Huber (2001)
Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.13
Page 2 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
1 Overall quality at a glance iO
The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY
The reported resolution of this entry is 4.20 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.
MetricWhole archive(#Entries)
EM structures(#Entries)
Ramachandran outliers 154571 4023Sidechain outliers 154315 3826
The table below summarises the geometric issues observed across the polymeric chains and their�t to the map. The red, orange, yellow and green segments on the bar indicate the fraction ofresidues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. Agrey segment 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 �t to the EMmap (all atom inclusion < 40%). The numeric value is given above the bar.
Mol Chain Length Quality of chain
1 4 1374
1 A 1374
1 B 1374
1 C 1374
1 D 1374
1 E 1374
1 F 1374
1 M 1374
1 N 1374Continued on next page...
Page 3 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
Continued from previous page...
Mol Chain Length Quality of chain
1 O 1374
1 S 1374
1 T 1374
1 U 1374
1 V 1374
1 W 1374
1 X 1374
2 0 112
2 1 112
2 2 112
2 3 112
2 G 112
2 H 112
2 I 112
2 J 112
2 K 112
2 L 112
2 P 112
2 Q 112
2 R 112
2 Y 112
2 Z 112
3 5 465
3 8 465
3 b 465Continued on next page...
Page 4 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
Continued from previous page...
Mol Chain Length Quality of chain
3 e 465
3 h 465
4 6 318
4 7 318
4 9 318
4 a 318
4 c 318
4 d 318
4 f 318
4 g 318
4 i 318
4 j 318
5 k 703
6 l 580
6 m 580
7 n 3139
7 o 3139
Page 5 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
2 Entry composition iO
There are 7 unique types of molecules in this entry. The entry contains 219702 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 Major capsid protein.
Mol Chain Residues Atoms AltConf Trace
1 A 1362Total C N O S10409 6575 1871 1909 54
0 0
1 B 1364Total C N O S10423 6585 1873 1911 54
0 0
1 C 1364Total C N O S10423 6585 1873 1911 54
0 0
1 D 1362Total C N O S10409 6575 1871 1909 54
0 0
1 E 1366Total C N O S10442 6595 1878 1915 54
0 0
1 F 1362Total C N O S10409 6575 1871 1909 54
0 0
1 M 1362Total C N O S10409 6575 1871 1909 54
0 0
1 N 1366Total C N O S10442 6595 1878 1915 54
0 0
1 O 1364Total C N O S10423 6585 1873 1911 54
0 0
1 S 1357Total C N O S10365 6547 1864 1900 54
0 0
1 T 1357Total C N O S10379 6553 1868 1904 54
0 0
1 U 1364Total C N O S10423 6585 1873 1911 54
0 0
1 V 1362Total C N O S10409 6575 1871 1909 54
0 0
1 W 1364Total C N O S10423 6585 1873 1911 54
0 0
1 X 1348Total C N O S10314 6516 1857 1888 53
0 0
1 4 1259Total C N O S9648 6103 1726 1769 50
0 0
� Molecule 2 is a protein called Small capsomere-interacting protein.
Page 6 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
Mol Chain Residues Atoms AltConf Trace
2 G 101Total C N O S774 488 146 137 3
0 0
2 H 101Total C N O S774 488 146 137 3
0 0
2 I 101Total C N O S774 488 146 137 3
0 0
2 J 101Total C N O S774 488 146 137 3
0 0
2 K 101Total C N O S774 488 146 137 3
0 0
2 L 101Total C N O S774 488 146 137 3
0 0
2 P 101Total C N O S774 488 146 137 3
0 0
2 Q 101Total C N O S774 488 146 137 3
0 0
2 R 101Total C N O S774 488 146 137 3
0 0
2 Y 101Total C N O S774 488 146 137 3
0 0
2 Z 101Total C N O S774 488 146 137 3
0 0
2 0 101Total C N O S774 488 146 137 3
0 0
2 1 101Total C N O S774 488 146 137 3
0 0
2 2 101Total C N O S774 488 146 137 3
0 0
2 3 101Total C N O S774 488 146 137 3
0 0
� Molecule 3 is a protein called Triplex capsid protein 1.
Mol Chain Residues Atoms AltConf Trace
3 5 353Total C N O S2724 1708 518 481 17
0 0
3 8 363Total C N O S2786 1741 531 496 18
0 0
3 b 363Total C N O S2786 1741 531 496 18
0 0
3 e 352Total C N O S2720 1706 517 480 17
0 0
3 h 353Total C N O S2724 1708 518 481 17
0 0
Page 7 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
� Molecule 4 is a protein called Triplex capsid protein 2.
Mol Chain Residues Atoms AltConf Trace
4 6 276Total C N O S2116 1354 375 380 7
0 0
4 7 308Total C N O S2341 1487 415 430 9
0 0
4 9 274Total C N O S2091 1338 370 376 7
0 0
4 a 308Total C N O S2341 1487 415 430 9
0 0
4 c 274Total C N O S2091 1338 370 376 7
0 0
4 d 308Total C N O S2341 1487 415 430 9
0 0
4 f 272Total C N O S2089 1337 371 374 7
0 0
4 g 308Total C N O S2341 1487 415 430 9
0 0
4 i 276Total C N O S2116 1354 375 380 7
0 0
4 j 308Total C N O S2341 1487 415 430 9
0 0
� Molecule 5 is a protein called Capsid vertex component 1.
Mol Chain Residues Atoms AltConf Trace
5 k 550Total C N O S4206 2674 764 747 21
0 0
� Molecule 6 is a protein called Capsid vertex component 2.
Mol Chain Residues Atoms AltConf Trace
6 l 94Total C N O S766 486 138 138 4
0 0
6 m 80Total C N O S654 413 124 115 2
0 0
� Molecule 7 is a protein called Large tegument protein deneddylase.
Mol Chain Residues Atoms AltConf Trace
7 n 47Total C N O S384 237 84 61 2
0 0
7 o 47Total C N O S384 237 84 61 2
0 0
Page 8 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
3 Residue-property plots iO
These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The�rst 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 �t 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.
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• Molecule 1: Major capsid protein
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Page 9 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 1: Major capsid protein
Chain C:
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• Molecule 1: Major capsid protein
Page 10 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 1: Major capsid protein
Chain E:
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Page 11 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 1: Major capsid protein
Chain F:
MET
ALA
ALA
PRO
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ARG
ASP
PRO
PRO
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• Molecule 1: Major capsid protein
Chain M:
MET
ALA
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PRO
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PRO
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Page 12 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 1: Major capsid protein
Chain N:
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• Molecule 1: Major capsid protein
Chain O:
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Page 13 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 1: Major capsid protein
Chain S:
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PRO
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ARG
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Page 14 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 1: Major capsid protein
Chain T:
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• Molecule 1: Major capsid protein
Chain U:
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Page 15 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 1: Major capsid protein
Chain V:
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Page 16 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 1: Major capsid protein
Chain W:
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• Molecule 1: Major capsid protein
Chain X:
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Page 17 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 1: Major capsid protein
Chain 4:
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VAL
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Page 18 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 2: Small capsomere-interacting protein
Chain G:
Page 19 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
MET
ALA
V3
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• Molecule 2: Small capsomere-interacting protein
Chain H:
MET
ALA
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F6
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R8
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PRO
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PRO
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PRO
• Molecule 2: Small capsomere-interacting protein
Chain I:
MET
ALA
V3
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PRO
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THR
PRO
GLY
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PRO
• Molecule 2: Small capsomere-interacting protein
Chain J:
MET
ALA
V3
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PRO
SER
THR
PRO
GLY
THR
PRO
• Molecule 2: Small capsomere-interacting protein
Chain K:
MET
ALA
V3
P4
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R8
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Page 20 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
D82
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PRO
• Molecule 2: Small capsomere-interacting protein
Chain L:
MET
ALA
V3
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Q5
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H7
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PRO
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PRO
GLY
THR
PRO
• Molecule 2: Small capsomere-interacting protein
Chain P:
MET
ALA
V3
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PRO
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THR
PRO
GLY
THR
PRO
• Molecule 2: Small capsomere-interacting protein
Chain Q:
MET
ALA
V3
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Q5
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D15
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PRO
SER
THR
PRO
GLY
THR
PRO
• Molecule 2: Small capsomere-interacting protein
Chain R:
MET
ALA
V3
P4
Q5
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PRO
SER
THR
PRO
GLY
THR
PRO
• Molecule 2: Small capsomere-interacting protein
Page 21 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
Chain Y:
MET
ALA
V3
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GLU
PRO
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THR
PRO
GLY
THR
PRO
• Molecule 2: Small capsomere-interacting protein
Chain Z:
MET
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GLU
PRO
SER
THR
PRO
GLY
THR
PRO
• Molecule 2: Small capsomere-interacting protein
Chain 0:
MET
ALA
V3
P4
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S10
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D15
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R18
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• Molecule 2: Small capsomere-interacting protein
Chain 1:
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• Molecule 2: Small capsomere-interacting protein
Chain 2:
MET
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D15
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Page 22 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 2: Small capsomere-interacting protein
Chain 3:
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• Molecule 3: Triplex capsid protein 1
Chain 5:
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LYS
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ASN
PRO
LEU
PRO
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VAL
TRP
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• Molecule 3: Triplex capsid protein 1
Chain 8:
MET
LYS
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Page 23 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 3: Triplex capsid protein 1
Chain b:
MET
LYS
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ASN
PRO
LEU
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VAL
TRP
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• Molecule 3: Triplex capsid protein 1
Chain e:
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Chain h:
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LYS
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VAL
TRP
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Page 24 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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• Molecule 4: Triplex capsid protein 2
Chain 6:
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• Molecule 4: Triplex capsid protein 2
Chain 7:
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Chain 9:
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Page 25 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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Chain a:
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• Molecule 4: Triplex capsid protein 2
Chain c:
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• Molecule 4: Triplex capsid protein 2
Chain d:
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Chain f:
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Page 26 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
PRO
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Chain g:
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Chain i:
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• Molecule 5: Capsid vertex component 1
Page 27 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
Chain k:M1
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• Molecule 6: Capsid vertex component 2
Chain l:
M1
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Page 28 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
ASP
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• Molecule 6: Capsid vertex component 2
Chain m:
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• Molecule 7: Large tegument protein deneddylase
Chain n:
Page 29 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
MET
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Page 30 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
ALA
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Page 31 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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Page 32 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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Page 33 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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Page 34 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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Page 35 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
4 Experimental information iO
Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, I DepositorNumber of particles used 28042 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−/Å
2) 25 Depositor
Minimum defocus (nm) 2000 DepositorMaximum defocus (nm) 2000 DepositorMagni�cation 24271 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 14.209 DepositorMinimum map value -10.389 DepositorAverage map value -0.000 DepositorMap value standard deviation 0.999 DepositorRecommended contour level 2.5 DepositorMap size (Å) 1318.3999, 1318.3999, 1318.3999 DepositorMap dimensions 1280, 1280, 1280 DepositorMap angles (◦) 90.0, 90.0, 90.0 DepositorPixel spacing (Å) 1.03, 1.03, 1.03 Depositor
Page 36 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
5 Model quality iO
5.1 Standard geometry iO
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 ChainBond lengths Bond angles
RMSZ #|Z| >5 RMSZ #|Z| >51 4 0.34 0/9878 0.57 3/13478 (0.0%)1 A 0.36 0/10664 0.58 3/14556 (0.0%)1 B 0.37 0/10680 0.59 1/14579 (0.0%)1 C 0.37 1/10680 (0.0%) 0.58 3/14579 (0.0%)1 D 0.39 0/10664 0.60 3/14556 (0.0%)1 E 0.39 0/10699 0.60 2/14605 (0.0%)1 F 0.38 0/10664 0.59 1/14556 (0.0%)1 M 0.38 0/10664 0.60 1/14556 (0.0%)1 N 0.39 0/10699 0.59 0/146051 O 0.37 0/10680 0.58 0/145791 S 0.36 0/10616 0.58 2/14487 (0.0%)1 T 0.38 0/10631 0.60 2/14507 (0.0%)1 U 0.39 1/10680 (0.0%) 0.60 1/14579 (0.0%)1 V 0.37 0/10664 0.59 3/14556 (0.0%)1 W 0.37 0/10680 0.58 0/145791 X 0.37 0/10567 0.59 3/14423 (0.0%)2 0 0.31 0/796 0.48 0/10872 1 0.31 0/796 0.48 0/10872 2 0.31 0/796 0.48 0/10872 3 0.31 0/796 0.48 0/10872 G 0.31 0/796 0.48 0/10872 H 0.31 0/796 0.48 0/10872 I 0.31 0/796 0.48 0/10872 J 0.31 0/796 0.48 0/10872 K 0.31 0/796 0.48 0/10872 L 0.31 0/796 0.48 0/10872 P 0.31 0/796 0.48 0/10872 Q 0.31 0/796 0.48 0/10872 R 0.31 0/796 0.48 0/10872 Y 0.31 0/796 0.48 0/10872 Z 0.31 0/796 0.48 0/10873 5 0.38 1/2795 (0.0%) 0.57 0/38103 8 0.37 0/2858 0.59 1/3895 (0.0%)3 b 0.37 0/2858 0.58 0/3895
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Mol ChainBond lengths Bond angles
RMSZ #|Z| >5 RMSZ #|Z| >53 e 0.35 0/2791 0.57 0/38053 h 0.35 0/2795 0.59 1/3810 (0.0%)4 6 0.36 0/2152 0.62 1/2939 (0.0%)4 7 0.36 0/2383 0.66 2/3259 (0.1%)4 9 0.36 0/2127 0.62 0/29064 a 0.38 0/2383 0.68 3/3259 (0.1%)4 c 0.36 0/2127 0.64 1/2906 (0.0%)4 d 0.38 0/2383 0.67 3/3259 (0.1%)4 f 0.36 0/2124 0.63 2/2900 (0.1%)4 g 0.37 0/2383 0.63 2/3259 (0.1%)4 i 0.35 0/2152 0.60 1/2939 (0.0%)4 j 0.36 0/2383 0.65 2/3259 (0.1%)5 k 0.33 0/4307 0.54 0/58666 l 0.33 0/786 0.52 0/10726 m 0.34 0/670 0.57 1/912 (0.1%)7 n 0.22 0/388 0.40 0/5217 o 0.22 0/388 0.40 0/521All All 0.37 3/224983 (0.0%) 0.59 48/307077 (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 4 0 21 A 0 21 B 0 21 C 0 11 D 0 21 E 0 11 F 0 21 M 0 21 N 0 21 O 0 11 S 0 11 T 0 21 U 0 51 V 0 31 W 0 41 X 0 13 8 0 1
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Mol Chain #Chirality outliers #Planarity outliers3 h 0 14 7 0 14 9 0 14 a 0 14 d 0 14 g 0 14 j 0 1All All 0 41
All (3) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)3 5 315 TYR CD1-CE1 -6.41 1.29 1.391 C 954 TYR CD1-CE1 -6.12 1.30 1.391 U 11 TYR CD2-CE2 -5.88 1.30 1.39
All (48) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 T 159 LEU CB-CG-CD1 -8.25 96.97 111.004 j 63 LEU CA-CB-CG 7.91 133.48 115.304 a 63 LEU CA-CB-CG 7.26 132.00 115.306 m 55 LEU CA-CB-CG 7.17 131.79 115.304 7 63 LEU CA-CB-CG 7.08 131.58 115.301 D 745 ARG NE-CZ-NH1 -7.07 116.77 120.301 V 159 LEU CA-CB-CG -6.97 99.27 115.301 B 159 LEU CA-CB-CG -6.90 99.42 115.301 E 159 LEU CB-CG-CD1 -6.77 99.48 111.003 h 259 LEU CA-CB-CG 6.74 130.79 115.304 a 39 ARG NE-CZ-NH2 -6.64 116.98 120.301 4 195 LEU CA-CB-CG 6.62 130.52 115.301 C 159 LEU CA-CB-CG -6.58 100.17 115.304 d 69 ARG NE-CZ-NH1 -6.54 117.03 120.301 A 159 LEU CB-CG-CD1 -6.32 100.27 111.001 E 27 ILE CG1-CB-CG2 -6.29 97.57 111.401 X 311 LEU CA-CB-CG 5.94 128.96 115.304 d 63 LEU CA-CB-CG 5.93 128.93 115.301 U 406 LEU CA-CB-CG 5.80 128.64 115.304 6 202 LEU CA-CB-CG 5.65 128.29 115.304 g 63 LEU CA-CB-CG 5.60 128.19 115.304 d 37 ILE CG1-CB-CG2 -5.57 99.15 111.401 V 103 LEU CA-CB-CG 5.55 128.06 115.30
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Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 8 259 LEU CA-CB-CG 5.54 128.03 115.301 M 745 ARG NE-CZ-NH1 -5.53 117.53 120.304 f 202 LEU CA-CB-CG 5.53 128.01 115.301 X 195 LEU CA-CB-CG 5.49 127.93 115.301 A 1102 LEU CA-CB-CG 5.48 127.91 115.301 T 195 LEU CA-CB-CG 5.42 127.77 115.301 S 1369 LEU CA-CB-CG 5.41 127.75 115.301 X 41 ARG NE-CZ-NH2 -5.35 117.63 120.301 F 103 LEU CA-CB-CG 5.34 127.58 115.301 S 195 LEU CA-CB-CG 5.34 127.58 115.304 g 37 ILE CG1-CB-CG2 -5.33 99.68 111.401 D 103 LEU CA-CB-CG 5.28 127.44 115.301 V 1102 LEU CA-CB-CG 5.27 127.42 115.304 7 37 ILE CG1-CB-CG2 -5.27 99.81 111.401 A 406 LEU CA-CB-CG 5.26 127.39 115.301 4 406 LEU CA-CB-CG 5.22 127.31 115.304 f 18 ARG NE-CZ-NH1 5.22 122.91 120.301 4 344 LEU CA-CB-CG 5.16 127.17 115.301 C 103 LEU CA-CB-CG 5.12 127.07 115.304 c 18 ARG NE-CZ-NH1 5.11 122.85 120.301 D 1102 LEU CA-CB-CG 5.11 127.04 115.304 a 39 ARG CG-CD-NE -5.06 101.17 111.804 i 202 LEU CA-CB-CG 5.01 126.82 115.301 C 406 LEU CA-CB-CG 5.00 126.81 115.304 j 37 ILE CG1-CB-CG2 -5.00 100.39 111.40
There are no chirality outliers.
All (41) planarity outliers are listed below:
Mol Chain Res Type Group1 4 112 ILE Peptide1 4 64 THR Peptide4 7 241 LEU Peptide3 8 281 PRO Peptide4 9 96 GLY Peptide1 A 133 PHE Peptide1 A 800 HIS Peptide1 B 133 PHE Peptide1 B 43 ARG Peptide1 C 133 PHE Peptide1 D 622 ASN Peptide1 D 800 HIS Peptide
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Mol Chain Res Type Group1 E 133 PHE Peptide1 F 133 PHE Peptide1 F 622 ASN Peptide1 M 133 PHE Peptide1 M 43 ARG Peptide1 N 133 PHE Peptide1 N 800 HIS Peptide1 O 133 PHE Peptide1 S 133 PHE Peptide1 T 133 PHE Peptide1 T 800 HIS Peptide1 U 133 PHE Peptide1 U 43 ARG Peptide1 U 44 SER Peptide1 U 54 PHE Peptide1 U 622 ASN Peptide1 V 133 PHE Peptide1 V 159 LEU Peptide1 V 800 HIS Peptide1 W 133 PHE Peptide1 W 43 ARG Peptide1 W 622 ASN Peptide1 W 800 HIS Peptide1 X 133 PHE Peptide4 a 241 LEU Peptide4 d 241 LEU Peptide4 g 241 LEU Peptide3 h 281 PRO Peptide4 j 241 LEU Peptide
5.2 Too-close contacts iO
Due to software issues we are unable to calculate clashes - this section is therefore empty.
5.3 Torsion angles iO
5.3.1 Protein backbone iO
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.
Page 41 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
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 4 1243/1374 (90%) 1169 (94%) 74 (6%) 0 100 100
1 A 1358/1374 (99%) 1262 (93%) 96 (7%) 0 100 100
1 B 1360/1374 (99%) 1258 (92%) 102 (8%) 0 100 100
1 C 1360/1374 (99%) 1265 (93%) 95 (7%) 0 100 100
1 D 1358/1374 (99%) 1246 (92%) 112 (8%) 0 100 100
1 E 1362/1374 (99%) 1254 (92%) 108 (8%) 0 100 100
1 F 1358/1374 (99%) 1244 (92%) 114 (8%) 0 100 100
1 M 1358/1374 (99%) 1244 (92%) 114 (8%) 0 100 100
1 N 1362/1374 (99%) 1253 (92%) 108 (8%) 1 (0%) 51 85
1 O 1360/1374 (99%) 1260 (93%) 100 (7%) 0 100 100
1 S 1353/1374 (98%) 1272 (94%) 81 (6%) 0 100 100
1 T 1349/1374 (98%) 1272 (94%) 77 (6%) 0 100 100
1 U 1360/1374 (99%) 1244 (92%) 116 (8%) 0 100 100
1 V 1358/1374 (99%) 1247 (92%) 111 (8%) 0 100 100
1 W 1360/1374 (99%) 1252 (92%) 108 (8%) 0 100 100
1 X 1344/1374 (98%) 1260 (94%) 84 (6%) 0 100 100
2 0 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 1 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 2 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 3 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 G 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 H 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 I 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 J 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 K 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 L 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 P 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 Q 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 R 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
2 Y 99/112 (88%) 94 (95%) 5 (5%) 0 100 100Continued on next page...
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Mol Chain Analysed Favoured Allowed Outliers Percentiles
2 Z 99/112 (88%) 94 (95%) 5 (5%) 0 100 100
3 5 349/465 (75%) 332 (95%) 17 (5%) 0 100 100
3 8 361/465 (78%) 340 (94%) 20 (6%) 1 (0%) 41 76
3 b 361/465 (78%) 341 (94%) 20 (6%) 0 100 100
3 e 348/465 (75%) 324 (93%) 24 (7%) 0 100 100
3 h 349/465 (75%) 326 (93%) 22 (6%) 1 (0%) 41 76
4 6 264/318 (83%) 249 (94%) 15 (6%) 0 100 100
4 7 304/318 (96%) 283 (93%) 19 (6%) 2 (1%) 22 62
4 9 264/318 (83%) 244 (92%) 20 (8%) 0 100 100
4 a 304/318 (96%) 277 (91%) 25 (8%) 2 (1%) 22 62
4 c 264/318 (83%) 246 (93%) 17 (6%) 1 (0%) 34 72
4 d 304/318 (96%) 274 (90%) 27 (9%) 3 (1%) 15 54
4 f 260/318 (82%) 238 (92%) 21 (8%) 1 (0%) 34 72
4 g 304/318 (96%) 276 (91%) 28 (9%) 0 100 100
4 i 264/318 (83%) 246 (93%) 18 (7%) 0 100 100
4 j 304/318 (96%) 273 (90%) 30 (10%) 1 (0%) 41 76
5 k 534/703 (76%) 514 (96%) 20 (4%) 0 100 100
6 l 92/580 (16%) 87 (95%) 5 (5%) 0 100 100
6 m 78/580 (13%) 77 (99%) 1 (1%) 0 100 100
7 n 45/3139 (1%) 45 (100%) 0 0 100 100
7 o 45/3139 (1%) 45 (100%) 0 0 100 100
All All 28486/37310 (76%) 26449 (93%) 2024 (7%) 13 (0%) 100 100
All (13) Ramachandran outliers are listed below:
Mol Chain Res Type3 8 282 ARG4 7 241 LEU4 d 241 LEU4 d 242 GLN3 h 282 ARG1 N 8 PRO4 7 242 GLN4 a 241 LEU4 a 242 GLN
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Mol Chain Res Type4 f 76 THR4 j 241 LEU4 d 55 GLY4 c 35 PRO
5.3.2 Protein sidechains iO
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 4 1003/1085 (92%) 1002 (100%) 1 (0%) 93 97
1 A 1076/1085 (99%) 1075 (100%) 1 (0%) 93 97
1 B 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97
1 C 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97
1 D 1076/1085 (99%) 1075 (100%) 1 (0%) 93 97
1 E 1080/1085 (100%) 1079 (100%) 1 (0%) 93 97
1 F 1076/1085 (99%) 1075 (100%) 1 (0%) 93 97
1 M 1076/1085 (99%) 1074 (100%) 2 (0%) 93 96
1 N 1080/1085 (100%) 1078 (100%) 2 (0%) 93 96
1 O 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97
1 S 1070/1085 (99%) 1069 (100%) 1 (0%) 93 97
1 T 1073/1085 (99%) 1072 (100%) 1 (0%) 93 97
1 U 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97
1 V 1076/1085 (99%) 1075 (100%) 1 (0%) 93 97
1 W 1078/1085 (99%) 1077 (100%) 1 (0%) 93 97
1 X 1069/1085 (98%) 1067 (100%) 2 (0%) 93 96
2 0 80/89 (90%) 80 (100%) 0 100 100
2 1 80/89 (90%) 80 (100%) 0 100 100
2 2 80/89 (90%) 80 (100%) 0 100 100
2 3 80/89 (90%) 80 (100%) 0 100 100Continued on next page...
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Mol Chain Analysed Rotameric Outliers Percentiles
2 G 80/89 (90%) 80 (100%) 0 100 100
2 H 80/89 (90%) 80 (100%) 0 100 100
2 I 80/89 (90%) 80 (100%) 0 100 100
2 J 80/89 (90%) 80 (100%) 0 100 100
2 K 80/89 (90%) 80 (100%) 0 100 100
2 L 80/89 (90%) 80 (100%) 0 100 100
2 P 80/89 (90%) 80 (100%) 0 100 100
2 Q 80/89 (90%) 80 (100%) 0 100 100
2 R 80/89 (90%) 80 (100%) 0 100 100
2 Y 80/89 (90%) 80 (100%) 0 100 100
2 Z 80/89 (90%) 80 (100%) 0 100 100
3 5 279/364 (77%) 279 (100%) 0 100 100
3 8 285/364 (78%) 285 (100%) 0 100 100
3 b 285/364 (78%) 285 (100%) 0 100 100
3 e 279/364 (77%) 279 (100%) 0 100 100
3 h 279/364 (77%) 279 (100%) 0 100 100
4 6 234/264 (89%) 234 (100%) 0 100 100
4 7 256/264 (97%) 256 (100%) 0 100 100
4 9 231/264 (88%) 231 (100%) 0 100 100
4 a 256/264 (97%) 256 (100%) 0 100 100
4 c 231/264 (88%) 231 (100%) 0 100 100
4 d 256/264 (97%) 255 (100%) 1 (0%) 91 94
4 f 231/264 (88%) 231 (100%) 0 100 100
4 g 256/264 (97%) 256 (100%) 0 100 100
4 i 234/264 (89%) 234 (100%) 0 100 100
4 j 256/264 (97%) 256 (100%) 0 100 100
5 k 429/529 (81%) 428 (100%) 1 (0%) 93 96
6 l 80/448 (18%) 80 (100%) 0 100 100
6 m 67/448 (15%) 66 (98%) 1 (2%) 65 80
7 n 41/2430 (2%) 40 (98%) 1 (2%) 49 69
7 o 41/2430 (2%) 40 (98%) 1 (2%) 49 69Continued on next page...
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Mol Chain Analysed Rotameric Outliers Percentiles
All All 22851/29440 (78%) 22827 (100%) 24 (0%) 93 97
All (24) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type1 A 519 ARG1 B 519 ARG1 C 519 ARG1 D 519 ARG1 E 519 ARG1 F 519 ARG1 M 272 ARG1 M 519 ARG1 N 519 ARG1 N 558 LEU1 O 519 ARG1 S 519 ARG1 T 519 ARG1 U 519 ARG1 V 519 ARG1 W 519 ARG1 X 451 ARG1 X 519 ARG1 4 519 ARG4 d 77 ARG5 k 103 ARG6 m 82 ARG7 n 3115 ARG7 o 3115 ARG
Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (345) suchsidechains are listed below:
Mol Chain Res Type1 A 63 ASN1 A 164 GLN1 A 168 ASN1 A 266 HIS1 A 429 HIS1 A 456 HIS1 A 485 ASN1 A 723 ASN
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Mol Chain Res Type1 A 777 ASN1 A 808 HIS1 A 863 HIS1 A 895 GLN1 A 961 HIS1 A 969 HIS1 A 1004 GLN1 A 1037 HIS1 A 1039 GLN1 A 1127 GLN1 A 1128 ASN1 A 1248 GLN1 B 63 ASN1 B 91 ASN1 B 164 GLN1 B 168 ASN1 B 266 HIS1 B 429 HIS1 B 456 HIS1 B 502 GLN1 B 717 GLN1 B 723 ASN1 B 782 GLN1 B 808 HIS1 B 863 HIS1 B 866 HIS1 B 961 HIS1 B 969 HIS1 B 1009 HIS1 B 1037 HIS1 B 1039 GLN1 C 63 ASN1 C 429 HIS1 C 456 HIS1 C 657 ASN1 C 658 ASN1 C 777 ASN1 C 788 GLN1 C 841 ASN1 C 866 HIS1 C 961 HIS1 C 1009 HIS
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Mol Chain Res Type1 C 1037 HIS1 C 1128 ASN1 C 1248 GLN1 C 1258 ASN1 C 1286 HIS1 D 91 ASN1 D 164 GLN1 D 168 ASN1 D 266 HIS1 D 315 ASN1 D 429 HIS1 D 456 HIS1 D 502 GLN1 D 503 GLN1 D 604 HIS1 D 696 HIS1 D 723 ASN1 D 724 HIS1 D 777 ASN1 D 788 GLN1 D 808 HIS1 D 841 ASN1 D 863 HIS1 D 969 HIS1 D 972 ASN1 D 1009 HIS1 D 1039 GLN1 D 1127 GLN1 D 1248 GLN1 D 1262 HIS1 E 164 GLN1 E 168 ASN1 E 266 HIS1 E 429 HIS1 E 456 HIS1 E 485 ASN1 E 502 GLN1 E 658 ASN1 E 785 HIS1 E 863 HIS1 E 969 HIS1 E 1009 HIS
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Mol Chain Res Type1 E 1037 HIS1 E 1117 ASN1 E 1127 GLN1 E 1128 ASN1 E 1248 GLN1 F 47 ASN1 F 63 ASN1 F 118 ASN1 F 456 HIS1 F 723 ASN1 F 863 HIS1 F 961 HIS1 F 1009 HIS1 F 1039 GLN1 F 1117 ASN1 F 1127 GLN1 F 1128 ASN1 F 1248 GLN2 J 57 GLN1 M 32 HIS1 M 266 HIS1 M 429 HIS1 M 456 HIS1 M 485 ASN1 M 658 ASN1 M 723 ASN1 M 785 HIS1 M 841 ASN1 M 863 HIS1 M 961 HIS1 M 969 HIS1 M 1009 HIS1 M 1037 HIS1 M 1039 GLN1 M 1083 HIS1 M 1090 ASN1 M 1127 GLN1 M 1128 ASN1 M 1248 GLN1 N 32 HIS1 N 63 ASN1 N 164 GLN
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Mol Chain Res Type1 N 168 ASN1 N 266 HIS1 N 315 ASN1 N 429 HIS1 N 456 HIS1 N 502 GLN1 N 723 ASN1 N 724 HIS1 N 777 ASN1 N 785 HIS1 N 808 HIS1 N 863 HIS1 N 961 HIS1 N 969 HIS1 N 1037 HIS1 N 1039 GLN1 N 1083 HIS1 N 1128 ASN1 O 266 HIS1 O 456 HIS1 O 502 GLN1 O 515 HIS1 O 658 ASN1 O 717 GLN1 O 723 ASN1 O 777 ASN1 O 866 HIS1 O 876 ASN1 O 961 HIS1 O 969 HIS1 O 1004 GLN1 O 1037 HIS1 O 1039 GLN1 O 1127 GLN1 O 1248 GLN1 S 100 HIS1 S 130 ASN1 S 156 HIS1 S 164 GLN1 S 168 ASN1 S 186 HIS1 S 266 HIS
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Mol Chain Res Type1 S 456 HIS1 S 515 HIS1 S 717 GLN1 S 723 ASN1 S 724 HIS1 S 863 HIS1 S 866 HIS1 S 961 HIS1 S 969 HIS1 S 1004 GLN1 S 1037 HIS1 S 1039 GLN1 S 1258 ASN1 T 63 ASN1 T 118 ASN1 T 156 HIS1 T 163 GLN1 T 164 GLN1 T 168 ASN1 T 266 HIS1 T 456 HIS1 T 717 GLN1 T 723 ASN1 T 724 HIS1 T 777 ASN1 T 788 GLN1 T 863 HIS1 T 866 HIS1 T 961 HIS1 T 969 HIS1 T 1004 GLN1 T 1037 HIS1 T 1039 GLN1 T 1090 ASN1 T 1128 ASN1 U 63 ASN1 U 163 GLN1 U 164 GLN1 U 168 ASN1 U 429 HIS1 U 456 HIS1 U 639 HIS
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Mol Chain Res Type1 U 717 GLN1 U 723 ASN1 U 777 ASN1 U 785 HIS1 U 808 HIS1 U 841 ASN1 U 863 HIS1 U 866 HIS1 U 895 GLN1 U 899 HIS1 U 900 ASN1 U 969 HIS1 U 1037 HIS1 U 1039 GLN1 V 63 ASN1 V 163 GLN1 V 164 GLN1 V 168 ASN1 V 266 HIS1 V 456 HIS1 V 502 GLN1 V 658 ASN1 V 723 ASN1 V 782 GLN1 V 841 ASN1 V 863 HIS1 V 866 HIS1 V 961 HIS1 V 969 HIS1 V 1004 GLN1 V 1009 HIS1 V 1037 HIS1 V 1039 GLN1 V 1127 GLN1 V 1248 GLN1 W 156 HIS1 W 266 HIS1 W 456 HIS1 W 723 ASN1 W 788 GLN1 W 808 HIS1 W 863 HIS
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Mol Chain Res Type1 W 866 HIS1 W 961 HIS1 W 969 HIS1 W 1009 HIS1 W 1037 HIS1 W 1039 GLN1 W 1127 GLN1 X 266 HIS1 X 429 HIS1 X 456 HIS1 X 658 ASN1 X 717 GLN1 X 723 ASN1 X 724 HIS1 X 777 ASN1 X 863 HIS1 X 866 HIS1 X 961 HIS1 X 969 HIS1 X 1004 GLN1 X 1037 HIS1 X 1039 GLN1 X 1117 ASN1 X 1128 ASN1 X 1262 HIS2 Y 68 HIS2 Z 68 HIS2 1 68 HIS1 4 100 HIS1 4 117 HIS1 4 186 HIS1 4 266 HIS1 4 340 GLN1 4 456 HIS1 4 515 HIS1 4 658 ASN1 4 717 GLN1 4 724 HIS1 4 785 HIS1 4 961 HIS1 4 969 HIS1 4 1004 GLN
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Mol Chain Res Type1 4 1009 HIS1 4 1037 HIS1 4 1258 ASN3 5 145 GLN3 5 235 HIS3 5 356 HIS4 6 281 HIS4 7 40 GLN4 7 193 GLN4 7 281 HIS3 8 120 GLN3 8 135 HIS3 8 356 HIS4 a 193 GLN4 a 242 GLN3 b 120 GLN3 b 135 HIS3 b 235 HIS3 b 237 HIS3 b 356 HIS3 b 369 ASN3 b 393 ASN4 d 193 GLN4 d 208 ASN3 e 120 GLN3 e 369 ASN4 f 238 ASN4 f 281 HIS4 g 99 ASN4 g 124 GLN4 g 193 GLN4 g 242 GLN3 h 120 GLN3 h 356 HIS4 i 110 ASN4 i 208 ASN4 i 238 ASN4 j 193 GLN5 k 157 ASN5 k 483 HIS5 k 506 GLN5 k 586 HIS
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Mol Chain Res Type6 m 15 HIS
5.3.3 RNA iO
There are no RNA molecules in this entry.
5.4 Non-standard residues in protein, DNA, RNA chains iO
There are no non-standard protein/DNA/RNA residues in this entry.
5.5 Carbohydrates iO
There are no monosaccharides in this entry.
5.6 Ligand geometry iO
There are no ligands in this entry.
5.7 Other polymers iO
There are no such residues in this entry.
5.8 Polymer linkage issues iO
There are no chain breaks in this entry.
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6 Map visualisation iO
This section contains visualisations of the EMDB entry EMD-7472. These are intended to permitvisual inspection of the internal detail of the map and identi�cation of artifacts.
6.1 Orthogonal projections iO
X Y Z
The images above show the map projected in three orthogonal projections, in greyscale.
6.2 Central slices iO
X Y Z
The images above show central slices of the map in three orthogonal directions, in greyscale.
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6.3 Largest variance slices iO
X Index: 875 Y Index: 753 Z Index: 612
The images above show the highest variance slices of the map in three orthogonal directions, ingreyscale.
6.4 Orthogonal surface views iO
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 2.5.This in conjunction with the slice images can indicate whether an appropriate contour level hasbeen selected.
6.5 Mask visualisation iO
This section was not generated. No masks were provided.
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7 Map analysis iO
This section contains the results of statistical analysis of the map.
7.1 Map-value distribution iO
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.
Page 58 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
7.2 Volume estimate iO
The volume at the recommended contour level is 60862 nm3; this corresponds to an approximatemass of 54978 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 59 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
7.3 Rotationally averaged power spectrum iO
Page 60 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
8 Fourier-Shell correlation iO
This section was not generated. No FSC curve or half maps provided.
Page 61 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
9 Map-model �t iO
This section contains information regarding the �t between EMDB map EMD-7472 and PDBmodel 6CGR. Per-residue inclusion information can be found in section 3 on page 8.
9.1 Map-model overlay iO
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 2.5 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 �t between the atomic model andthe map.
Page 62 Full wwPDB EM Map/Model Validation Report EMD-7472, 6CGR
9.2 Atom inclusion iO
At the recommended contour level, 74% of all backbone atoms, 57% of all non-hydrogen atoms,are inside the map.