26
Full wwPDB EM Validation Report iO
Dec 6, 2020 � 07:48 AM GMT
PDB ID : 6TIKEMDB ID : EMD-10316
Title : Hepatitis B virus core shell�virus-like particle with NadA epitopeAuthors : Roseman, A.M.; Colllins, R.F.; Derrick, J.P.
Deposited on : 2019-11-22Resolution : 3.40 Å(reported)
Based on initial model : 1QGT
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 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.dev61MolProbity : 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) : 2.15.1
Page 2 Full wwPDB EM Validation Report EMD-10316, 6TIK
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 3.40 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.
MetricWhole 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 �tto 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 �t to the EMmap (all-atom inclusion < 40%). The numeric value is given above the bar.
Mol Chain Length Quality of chain
1 A 589
1 B 589
1 C 589
1 D 589
Page 3 Full wwPDB EM Validation Report EMD-10316, 6TIK
2 Entry composition iO
There is only 1 type of molecule in this entry. The entry contains 4420 atoms, of which 0 arehydrogens 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 Capsid protein,Putative adhesin/invasin,Capsid protein,FactorH-binding protein.
Mol Chain Residues Atoms AltConf Trace
1 C 137Total C N O S1101 715 183 197 6
0 0
1 D 138Total C N O S1109 721 184 198 6
0 0
1 B 138Total C N O S1109 721 184 198 6
0 0
1 A 137Total C N O S1101 715 183 197 6
0 0
There are 164 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceC 79 GLY - linker UNP Q67855C 80 GLY - linker UNP Q67855C 81 GLY - linker UNP Q67855C 82 GLY - linker UNP Q67855C 83 SER - linker UNP Q67855C 84 GLY - linker UNP Q67855C 85 GLY - linker UNP Q67855C 86 GLY - linker UNP Q67855C 87 GLY - linker UNP Q67855C 88 SER - linker UNP Q67855C 373 GLU - linker UNP D3IRF1C 374 PHE - linker UNP D3IRF1C 375 GLY - linker UNP D3IRF1C 376 GLY - linker UNP D3IRF1C 377 GLY - linker UNP D3IRF1C 378 GLY - linker UNP D3IRF1C 379 SER - linker UNP D3IRF1C 380 GLY - linker UNP D3IRF1C 381 GLY - linker UNP D3IRF1C 382 GLY - linker UNP D3IRF1C 383 GLY - linker UNP D3IRF1
Continued on next page...
Page 4 Full wwPDB EM Validation Report EMD-10316, 6TIK
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Chain Residue Modelled Actual Comment ReferenceC 384 SER - linker UNP D3IRF1C 453 GLY - linker UNP Q67855C 454 SER - linker UNP Q67855C 455 GLY - linker UNP Q67855C 456 GLY - linker UNP Q67855C 457 GLY - linker UNP Q67855C 458 THR - linker UNP Q67855C 577 LYS - expression tag UNP Q6QCC2C 578 LEU - expression tag UNP Q6QCC2C 579 GLY - expression tag UNP Q6QCC2C 580 GLY - expression tag UNP Q6QCC2C 581 GLY - expression tag UNP Q6QCC2C 582 TRP - expression tag UNP Q6QCC2C 583 SER - expression tag UNP Q6QCC2C 584 HIS - expression tag UNP Q6QCC2C 585 PRO - expression tag UNP Q6QCC2C 586 GLN - expression tag UNP Q6QCC2C 587 PHE - expression tag UNP Q6QCC2C 588 GLU - expression tag UNP Q6QCC2C 589 LYS - expression tag UNP Q6QCC2D 79 GLY - linker UNP Q67855D 80 GLY - linker UNP Q67855D 81 GLY - linker UNP Q67855D 82 GLY - linker UNP Q67855D 83 SER - linker UNP Q67855D 84 GLY - linker UNP Q67855D 85 GLY - linker UNP Q67855D 86 GLY - linker UNP Q67855D 87 GLY - linker UNP Q67855D 88 SER - linker UNP Q67855D 373 GLU - linker UNP D3IRF1D 374 PHE - linker UNP D3IRF1D 375 GLY - linker UNP D3IRF1D 376 GLY - linker UNP D3IRF1D 377 GLY - linker UNP D3IRF1D 378 GLY - linker UNP D3IRF1D 379 SER - linker UNP D3IRF1D 380 GLY - linker UNP D3IRF1D 381 GLY - linker UNP D3IRF1D 382 GLY - linker UNP D3IRF1D 383 GLY - linker UNP D3IRF1D 384 SER - linker UNP D3IRF1
Continued on next page...
Page 5 Full wwPDB EM Validation Report EMD-10316, 6TIK
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Chain Residue Modelled Actual Comment ReferenceD 453 GLY - linker UNP Q67855D 454 SER - linker UNP Q67855D 455 GLY - linker UNP Q67855D 456 GLY - linker UNP Q67855D 457 GLY - linker UNP Q67855D 458 THR - linker UNP Q67855D 577 LYS - expression tag UNP Q6QCC2D 578 LEU - expression tag UNP Q6QCC2D 579 GLY - expression tag UNP Q6QCC2D 580 GLY - expression tag UNP Q6QCC2D 581 GLY - expression tag UNP Q6QCC2D 582 TRP - expression tag UNP Q6QCC2D 583 SER - expression tag UNP Q6QCC2D 584 HIS - expression tag UNP Q6QCC2D 585 PRO - expression tag UNP Q6QCC2D 586 GLN - expression tag UNP Q6QCC2D 587 PHE - expression tag UNP Q6QCC2D 588 GLU - expression tag UNP Q6QCC2D 589 LYS - expression tag UNP Q6QCC2B 79 GLY - linker UNP Q67855B 80 GLY - linker UNP Q67855B 81 GLY - linker UNP Q67855B 82 GLY - linker UNP Q67855B 83 SER - linker UNP Q67855B 84 GLY - linker UNP Q67855B 85 GLY - linker UNP Q67855B 86 GLY - linker UNP Q67855B 87 GLY - linker UNP Q67855B 88 SER - linker UNP Q67855B 373 GLU - linker UNP D3IRF1B 374 PHE - linker UNP D3IRF1B 375 GLY - linker UNP D3IRF1B 376 GLY - linker UNP D3IRF1B 377 GLY - linker UNP D3IRF1B 378 GLY - linker UNP D3IRF1B 379 SER - linker UNP D3IRF1B 380 GLY - linker UNP D3IRF1B 381 GLY - linker UNP D3IRF1B 382 GLY - linker UNP D3IRF1B 383 GLY - linker UNP D3IRF1B 384 SER - linker UNP D3IRF1B 453 GLY - linker UNP Q67855
Continued on next page...
Page 6 Full wwPDB EM Validation Report EMD-10316, 6TIK
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Chain Residue Modelled Actual Comment ReferenceB 454 SER - linker UNP Q67855B 455 GLY - linker UNP Q67855B 456 GLY - linker UNP Q67855B 457 GLY - linker UNP Q67855B 458 THR - linker UNP Q67855B 577 LYS - expression tag UNP Q6QCC2B 578 LEU - expression tag UNP Q6QCC2B 579 GLY - expression tag UNP Q6QCC2B 580 GLY - expression tag UNP Q6QCC2B 581 GLY - expression tag UNP Q6QCC2B 582 TRP - expression tag UNP Q6QCC2B 583 SER - expression tag UNP Q6QCC2B 584 HIS - expression tag UNP Q6QCC2B 585 PRO - expression tag UNP Q6QCC2B 586 GLN - expression tag UNP Q6QCC2B 587 PHE - expression tag UNP Q6QCC2B 588 GLU - expression tag UNP Q6QCC2B 589 LYS - expression tag UNP Q6QCC2A 79 GLY - linker UNP Q67855A 80 GLY - linker UNP Q67855A 81 GLY - linker UNP Q67855A 82 GLY - linker UNP Q67855A 83 SER - linker UNP Q67855A 84 GLY - linker UNP Q67855A 85 GLY - linker UNP Q67855A 86 GLY - linker UNP Q67855A 87 GLY - linker UNP Q67855A 88 SER - linker UNP Q67855A 373 GLU - linker UNP D3IRF1A 374 PHE - linker UNP D3IRF1A 375 GLY - linker UNP D3IRF1A 376 GLY - linker UNP D3IRF1A 377 GLY - linker UNP D3IRF1A 378 GLY - linker UNP D3IRF1A 379 SER - linker UNP D3IRF1A 380 GLY - linker UNP D3IRF1A 381 GLY - linker UNP D3IRF1A 382 GLY - linker UNP D3IRF1A 383 GLY - linker UNP D3IRF1A 384 SER - linker UNP D3IRF1A 453 GLY - linker UNP Q67855A 454 SER - linker UNP Q67855
Continued on next page...
Page 7 Full wwPDB EM Validation Report EMD-10316, 6TIK
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Chain Residue Modelled Actual Comment ReferenceA 455 GLY - linker UNP Q67855A 456 GLY - linker UNP Q67855A 457 GLY - linker UNP Q67855A 458 THR - linker UNP Q67855A 577 LYS - expression tag UNP Q6QCC2A 578 LEU - expression tag UNP Q6QCC2A 579 GLY - expression tag UNP Q6QCC2A 580 GLY - expression tag UNP Q6QCC2A 581 GLY - expression tag UNP Q6QCC2A 582 TRP - expression tag UNP Q6QCC2A 583 SER - expression tag UNP Q6QCC2A 584 HIS - expression tag UNP Q6QCC2A 585 PRO - expression tag UNP Q6QCC2A 586 GLN - expression tag UNP Q6QCC2A 587 PHE - expression tag UNP Q6QCC2A 588 GLU - expression tag UNP Q6QCC2A 589 LYS - expression tag UNP Q6QCC2
Page 8 Full wwPDB EM Validation Report EMD-10316, 6TIK
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.
• Molecule 1: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding pro-tein
Chain C:
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• Molecule 1: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding pro-tein
Chain D:
M1
D2
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Page 9 Full wwPDB EM Validation Report EMD-10316, 6TIK
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ASP
ILE
ALA
THR
ASN
LYS
ALA
ASP
ILE
ALA
LYS
ASN
SER
ALA
ARG
ILE
ASP
SER
LEU
ASP
LYS
ASN
VAL
ALA
ASN
LEU
ARG
LYS
GLU
THR
ARG
GLN
GLY
LEU
ALA
GLU
GLN
ALA
ALA
LEU
SER
GLY
LEU
PHE
GLN
PRO
TYR
ASN
VAL
GLY
GLU
PHE
GLY
GLY
GLY
GLY
SER
GLY
GLY
GLY
GLY
SER
R385�
V388
N393�
H407
L446�
PRO
GLU
THR
THR
VAL
VAL
GLY
SER
GLY
GLY
GLY
THR
HIS
THR
SER
PHE
ASP
LYS
LEU
PRO
GLU
GLY
GLY
ARG
ALA
THR
TYR
ARG
GLY
THR
ALA
PHE
GLY
SER
ASP
ASP
ALA
GLY
GLY
LYS
LEU
THR
TYR
THR
ILE
ASP
PHE
ALA
ALA
LYS
GLN
GLY
ASN
GLY
LYS
ILE
GLU
HIS
LEU
LYS
SER
PRO
GLU
LEU
ASN
VAL
ASP
LEU
ALA
ALA
ALA
ASP
ILE
LYS
PRO
ASP
GLY
LYS
ARG
HIS
ALA
VAL
ILE
SER
GLY
SER
VAL
LEU
TYR
ASN
GLN
ALA
GLU
LYS
GLY
SER
TYR
SER
LEU
GLY
ILE
PHE
GLY
GLY
LYS
ALA
GLN
GLU
VAL
ALA
GLY
SER
ALA
GLU
VAL
LYS
THR
VAL
ASN
GLY
ILE
ARG
HIS
ILE
GLY
LEU
ALA
ALA
LYS
GLN
LYS
LEU
GLY
GLY
GLY
TRP
SER
HIS
PRO
GLN
PHE
GLU
LYS
Page 10 Full wwPDB EM Validation Report EMD-10316, 6TIK
• Molecule 1: Capsid protein,Putative adhesin/invasin,Capsid protein,Factor H-binding pro-tein
Chain A:
M1
K7
E8
L30
L42
E43
S44
P45
E46
H47
C48
�
L55
R56
W62
W71
L76
GLU
ASP
GLY
GLY
GLY
GLY
SER
GLY
GLY
GLY
GLY
SER
ALA
THR
SER
ASP
ASP
ASP
VAL
LYS
LYS
ALA
ALA
THR
VAL
ALA
ILE
VAL
ALA
ALA
TYR
ASN
ASN
GLY
GLN
GLU
ILE
ASN
GLY
PHE
LYS
ALA
GLY
GLU
THR
ILE
TYR
ASP
ILE
GLY
GLU
ASP
GLY
THR
ILE
THR
GLN
LYS
ASP
ALA
THR
ALA
ALA
ASP
VAL
GLU
ALA
ASP
ASP
PHE
LYS
GLY
LEU
GLY
LEU
LYS
LYS
VAL
VAL
THR
ASN
LEU
THR
LYS
THR
VAL
ASN
GLU
ASN
LYS
GLN
ASN
VAL
ASP
ALA
LYS
VAL
LYS
ALA
ALA
GLU
SER
GLU
ILE
GLU
LYS
LEU
THR
THR
LYS
LEU
ALA
ASP
THR
ASP
ALA
ALA
LEU
ALA
ASP
THR
ASP
ALA
ALA
LEU
ASP
GLU
THR
THR
ASN
ALA
LEU
ASN
LYS
LEU
GLY
GLU
ASN
ILE
THR
THR
PHE
ALA
GLU
GLU
THR
LYS
THR
ASN
ILE
VAL
LYS
ILE
ASP
GLU
LYS
LEU
GLU
ALA
VAL
ALA
ASP
THR
VAL
ASP
LYS
HIS
ALA
GLU
ALA
PHE
ASN
ASP
ILE
ALA
ASP
SER
LEU
ASP
GLU
THR
ASN
THR
LYS
ALA
ASP
GLU
ALA
VAL
LYS
THR
ALA
ASN
GLU
ALA
LYS
GLN
THR
ALA
GLU
GLU
THR
LYS
GLN
ASN
VAL
ASP
ALA
LYS
VAL
LYS
ALA
ALA
GLU
THR
ALA
ALA
GLY
LYS
ALA
GLU
ALA
ALA
ALA
GLY
THR
ALA
ASN
THR
ALA
ALA
ASP
LYS
ALA
GLU
ALA
VAL
ALA
ALA
LYS
VAL
THR
ASP
ILE
LYS
ALA
ASP
ILE
ALA
THR
ASN
LYS
ALA
ASP
ILE
ALA
LYS
ASN
SER
ALA
ARG
ILE
ASP
SER
LEU
ASP
LYS
ASN
VAL
ALA
ASN
LEU
ARG
LYS
GLU
THR
ARG
GLN
GLY
LEU
ALA
GLU
GLN
ALA
ALA
LEU
SER
GLY
LEU
PHE
GLN
PRO
TYR
ASN
VAL
GLY
GLU
PHE
GLY
GLY
GLY
GLY
SER
GLY
GLY
GLY
GLY
SER
R385�
V388
I400
R401
I408
T445
LEU
PRO
GLU
THR
THR
VAL
VAL
GLY
SER
GLY
GLY
GLY
THR
HIS
THR
SER
PHE
ASP
LYS
LEU
PRO
GLU
GLY
GLY
ARG
ALA
THR
TYR
ARG
GLY
THR
ALA
PHE
GLY
SER
ASP
ASP
ALA
GLY
GLY
LYS
LEU
THR
TYR
THR
ILE
ASP
PHE
ALA
ALA
LYS
GLN
GLY
ASN
GLY
LYS
ILE
GLU
HIS
LEU
LYS
SER
PRO
GLU
LEU
ASN
VAL
ASP
LEU
ALA
ALA
ALA
ASP
ILE
LYS
PRO
ASP
GLY
LYS
ARG
HIS
ALA
VAL
ILE
SER
GLY
SER
VAL
LEU
TYR
ASN
GLN
ALA
GLU
LYS
GLY
SER
TYR
SER
LEU
GLY
ILE
PHE
GLY
GLY
LYS
ALA
GLN
GLU
VAL
ALA
GLY
SER
ALA
GLU
VAL
LYS
THR
VAL
ASN
GLY
ILE
ARG
HIS
ILE
GLY
LEU
ALA
ALA
LYS
GLN
LYS
LEU
GLY
GLY
GLY
TRP
SER
HIS
PRO
GLN
PHE
GLU
LYS
Page 11 Full wwPDB EM Validation Report EMD-10316, 6TIK
4 Experimental information iO
Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, I DepositorNumber of particles used 8598 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) 79 Depositor
Minimum defocus (nm) 424 DepositorMaximum defocus (nm) 3840 DepositorMagni�cation 100719 DepositorImage detector FEI FALCON III (4k x 4k) DepositorMaximum map value 4.963 DepositorMinimum map value -1.180 DepositorAverage map value 0.011 DepositorMap value standard deviation 0.233 DepositorRecommended contour level 1.5 DepositorMap size (Å) 711.68, 711.68, 711.68 wwPDBMap dimensions 512, 512, 512 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.39, 1.39, 1.39 Depositor
Page 12 Full wwPDB EM Validation Report EMD-10316, 6TIK
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 anglesRMSZ #|Z| >5 RMSZ #|Z| >5
1 A 0.41 0/1133 0.47 0/15491 B 0.41 0/1141 0.53 1/1560 (0.1%)1 C 0.41 0/1133 0.50 0/15491 D 0.41 0/1141 0.51 0/1560All All 0.41 0/4548 0.50 1/6218 (0.0%)
There are no bond length outliers.
All (1) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 B 446 LEU CA-CB-CG 5.47 127.89 115.30
There are no chirality outliers.
There are no planarity outliers.
5.2 Too-close contacts iO
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 1101 0 1087 12 01 B 1109 0 1098 11 01 C 1101 0 1087 15 01 D 1109 0 1098 12 0All All 4420 0 4370 40 0
The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 5.
Page 13 Full wwPDB EM Validation Report EMD-10316, 6TIK
All (40) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:B:8:GLU:OE2 1:A:56:ARG:NH1 2.32 0.631:D:21:SER:HB2 1:D:398:LEU:HD11 1.84 0.601:C:7:LYS:HG2 1:D:45:PRO:HB3 1.85 0.58
1:C:72:VAL:HG13 1:C:76:LEU:HD12 1.87 0.571:D:24:PHE:O 1:D:401:ARG:NH1 2.38 0.561:B:7:LYS:HG2 1:A:45:PRO:HB3 1.87 0.561:C:41:ALA:O 1:C:56:ARG:NH2 2.38 0.561:A:44:SER:OG 1:A:46:GLU:OE1 2.24 0.551:A:42:LEU:O 1:A:56:ARG:NE 2.40 0.53
1:C:20:PRO:HG2 1:C:23:PHE:HB2 1.92 0.511:B:71:TRP:O 1:B:75:ASN:ND2 2.39 0.51
1:B:56:ARG:NH1 1:A:8:GLU:OE1 2.44 0.501:B:45:PRO:HB3 1:A:7:LYS:HG2 1.94 0.501:C:423:VAL:HG13 1:B:37:LEU:HD22 1.92 0.501:C:425:PHE:HE1 1:C:440:ALA:HB1 1.78 0.491:C:56:ARG:NH1 1:D:8:GLU:OE1 2.45 0.491:D:444:SER:OG 1:D:445:THR:N 2.46 0.491:C:19:LEU:HD22 1:C:425:PHE:HD2 1.80 0.461:C:18:PHE:O 1:C:430:ARG:NH1 2.43 0.46
1:C:45:PRO:HB3 1:D:7:LYS:HG2 1.97 0.461:C:30:LEU:HD12 1:C:408:ILE:HD12 1.97 0.451:A:62:TRP:HB2 1:A:400:ILE:HG21 1.99 0.451:A:42:LEU:HD21 1:A:55:LEU:HD23 1.97 0.451:D:30:LEU:HD12 1:D:408:ILE:HD12 2.00 0.431:D:19:LEU:HD21 1:D:422:LEU:HD22 2.01 0.431:C:38:TYR:OH 1:C:412:THR:OG1 2.35 0.421:D:4:ASP:HB3 1:D:7:LYS:HB2 2.01 0.42
1:B:388:VAL:HG22 1:A:71:TRP:HZ3 1.84 0.421:A:30:LEU:HD12 1:A:408:ILE:HD12 2.02 0.421:B:71:TRP:HZ3 1:A:388:VAL:HG22 1.85 0.421:C:6:TYR:HB3 1:C:11:ALA:HB3 2.01 0.421:B:55:LEU:HD13 1:B:407:HIS:HB2 2.02 0.411:D:20:PRO:HG2 1:D:23:PHE:HB2 2.01 0.411:A:401:ARG:HH11 1:A:401:ARG:HD2 1.77 0.411:B:72:VAL:HG11 1:B:388:VAL:HG21 2.02 0.411:D:72:VAL:HG11 1:D:388:VAL:HG21 2.03 0.411:B:51:HIS:O 1:B:55:LEU:N 2.54 0.40
1:C:24:PHE:CE2 1:C:402:GLN:HG2 2.57 0.401:C:392:VAL:O 1:C:397:GLY:N 2.53 0.40
1:D:27:VAL:HG11 1:D:62:TRP:CE2 2.57 0.40
Page 14 Full wwPDB EM Validation Report EMD-10316, 6TIK
There are no symmetry-related clashes.
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.
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 133/589 (23%) 132 (99%) 1 (1%) 0 100 100
1 B 134/589 (23%) 131 (98%) 3 (2%) 0 100 100
1 C 133/589 (23%) 132 (99%) 1 (1%) 0 100 100
1 D 134/589 (23%) 132 (98%) 2 (2%) 0 100 100
All All 534/2356 (23%) 527 (99%) 7 (1%) 0 100 100
There are no Ramachandran outliers to report.
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 A 122/449 (27%) 122 (100%) 0 100 100
1 B 123/449 (27%) 123 (100%) 0 100 100
1 C 122/449 (27%) 121 (99%) 1 (1%) 81 91
1 D 123/449 (27%) 122 (99%) 1 (1%) 81 91
All All 490/1796 (27%) 488 (100%) 2 (0%) 91 95
All (2) residues with a non-rotameric sidechain are listed below:
Page 15 Full wwPDB EM Validation Report EMD-10316, 6TIK
Mol Chain Res Type1 C 385 ARG1 D 393 ASN
Sometimes sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (3) suchsidechains are listed below:
Mol Chain Res Type1 D 390 ASN1 D 393 ASN1 A 407 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.
Page 16 Full wwPDB EM Validation Report EMD-10316, 6TIK
6 Map visualisation iO
This section contains visualisations of the EMDB entry EMD-10316. These allow visual inspectionof the internal detail of the map and identi�cation 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 iO
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.
Page 17 Full wwPDB EM Validation Report EMD-10316, 6TIK
6.2 Central slices iO
6.2.1 Primary map
X Index: 256 Y Index: 256 Z Index: 256
6.2.2 Raw map
X Index: 256 Y Index: 256 Z Index: 256
The images above show central slices of the map in three orthogonal directions.
Page 18 Full wwPDB EM Validation Report EMD-10316, 6TIK
6.3 Largest variance slices iO
6.3.1 Primary map
X Index: 275 Y Index: 275 Z Index: 237
6.3.2 Raw map
X Index: 276 Y Index: 276 Z Index: 236
The images above show the largest variance slices of the map in three orthogonal directions.
Page 19 Full wwPDB EM Validation Report EMD-10316, 6TIK
6.4 Orthogonal surface views iO
6.4.1 Primary map
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 1.5.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.
6.5 Mask visualisation iO
This section was not generated. No masks/segmentation were deposited.
Page 20 Full wwPDB EM Validation Report EMD-10316, 6TIK
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 21 Full wwPDB EM Validation Report EMD-10316, 6TIK
7.2 Volume estimate iO
The volume at the recommended contour level is 1945 nm3; this corresponds to an approximatemass of 1757 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 22 Full wwPDB EM Validation Report EMD-10316, 6TIK
7.3 Rotationally averaged power spectrum iO
*Reported resolution corresponds to spatial frequency of 0.294 Å−1
Page 23 Full wwPDB EM Validation Report EMD-10316, 6TIK
8 Fourier-Shell correlation iO
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-o� and 0.5 cut-o�.
8.1 FSC iO
*Reported resolution corresponds to spatial frequency of 0.294 Å−1
Page 24 Full wwPDB EM Validation Report EMD-10316, 6TIK
8.2 Resolution estimates iO
Resolution estimate (Å)Estimation criterion (FSC cut-o�)0.143 0.5 Half-bit
Reported by author 3.40 - -Author-provided FSC curve - - -
Calculated* 4.35 7.03 4.44
*Resolution estimate based on FSC curve calculated by comparison of deposited half-maps. Thevalue from deposited half-maps intersecting FSC 0.143 CUT-OFF 4.35 di�ers from the reportedvalue 3.4 by more than 10 %
Page 25 Full wwPDB EM Validation Report EMD-10316, 6TIK
9 Map-model �t iO
This section contains information regarding the �t between EMDB map EMD-10316 and PDBmodel 6TIK. 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 1.5 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 26 Full wwPDB EM Validation Report EMD-10316, 6TIK
9.2 Atom inclusion iO
At the recommended contour level, 96% of all backbone atoms, 80% of all non-hydrogen atoms,are inside the map.
