full wwpdb/emdatabank em map/model validation...
TRANSCRIPT
Full wwPDB/EMDataBank EM Map/Model ValidationReport i○
Aug 28, 2019 – 09:44 AM EDT
PDB ID : 6PXVEMDB ID: : EMD-20522
Title : Cryo-EM structure of full-length insulin receptor bound to 4 insulin. 3D re-finement was focused on the extracellular region.
Authors : Uchikawa, E.; Choi, E.; Shang, G.J.; Yu, H.T.; Bai, X.C.Deposited on : 2019-07-27
Resolution : 3.20 Å(reported)
This is a Full wwPDB/EMDataBank EM Map/Model Validation Reportfor a publicly released PDB/EMDB 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.
MolProbity : 4.02b-467Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)
Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et. al. (1996)
Validation Pipeline (wwPDB-VP) : 2.4
Page 2 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV
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 3.20 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.
Metric Whole archive(#Entries)
EM structures(#Entries)
Clashscore 136327 1886Ramachandran outliers 132723 1663
Sidechain outliers 132532 1531
The table below summarises the geometric issues observed across the polymeric chains. The red,orange, yellow and green segments on the bar indicate the fraction of residues that contain outliersfor >=3, 2, 1 and 0 types of geometric quality criteria. A grey segment represents the fractionof residues that are not modelled. The numeric value for each fraction is indicated below thecorresponding segment, with a dot representing fractions <=5%
Mol Chain Length Quality of chain
1 A 1354
1 C 1354
2 D 74
2 E 74
2 F 74
2 G 74
Page 3 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV
2 Entry composition i○
There are 2 unique types of molecules in this entry. The entry contains 14774 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 Insulin receptor.
Mol Chain Residues Atoms AltConf Trace
1 A 823 Total C N O S6664 4231 1149 1236 48 0 0
1 C 823 Total C N O S6664 4231 1149 1236 48 0 0
There are 36 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA 960 PHE TYR conflict UNP P06213A 962 THR SER conflict UNP P06213A 1120 ASN ASP conflict UNP P06213A 1333 ALA ARG conflict UNP P06213A 1334 ALA ILE conflict UNP P06213A 1335 ALA LEU conflict UNP P06213A 1337 ALA LEU conflict UNP P06213A 1344 LEU - expression tag UNP P06213A 1345 GLU - expression tag UNP P06213A 1346 SER - expression tag UNP P06213A 1347 SER - expression tag UNP P06213A 1348 GLY - expression tag UNP P06213A 1349 LEU - expression tag UNP P06213A 1350 GLU - expression tag UNP P06213A 1351 VAL - expression tag UNP P06213A 1352 LEU - expression tag UNP P06213A 1353 PHE - expression tag UNP P06213A 1354 GLN - expression tag UNP P06213C 960 PHE TYR conflict UNP P06213C 962 THR SER conflict UNP P06213C 1120 ASN ASP conflict UNP P06213C 1333 ALA ARG conflict UNP P06213C 1334 ALA ILE conflict UNP P06213C 1335 ALA LEU conflict UNP P06213C 1337 ALA LEU conflict UNP P06213C 1344 LEU - expression tag UNP P06213
Continued on next page...
Page 4 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV
Continued from previous page...Chain Residue Modelled Actual Comment Reference
C 1345 GLU - expression tag UNP P06213C 1346 SER - expression tag UNP P06213C 1347 SER - expression tag UNP P06213C 1348 GLY - expression tag UNP P06213C 1349 LEU - expression tag UNP P06213C 1350 GLU - expression tag UNP P06213C 1351 VAL - expression tag UNP P06213C 1352 LEU - expression tag UNP P06213C 1353 PHE - expression tag UNP P06213C 1354 GLN - expression tag UNP P06213
• Molecule 2 is a protein called Insulin.
Mol Chain Residues Atoms AltConf Trace
2 D 48 Total C N O S376 238 61 71 6 0 0
2 E 48 Total C N O S376 238 61 71 6 0 0
2 F 44 Total C N O S347 220 56 65 6 0 0
2 G 44 Total C N O S347 220 56 65 6 0 0
Page 5 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV
3 Residue-property plots i○
These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic fora chain summarises the proportions of the various outlier classes displayed in the second graphic.The second graphic shows the sequence view annotated by issues in geometry. Residues are color-coded according to the number of geometric quality criteria for which they contain at least oneoutlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretches of 2 or more consecutiveresidues without any outlier are shown as a green connector. Residues present in the sample, butnot in the model, are shown in grey.
• Molecule 1: Insulin receptor
Chain A:
H1 R14
N15
L20
L23
I29
L49
V99
H100
L101
K102
N111
R114
K121
L125
Y144
I145
V146
T162
ALA
LYS
GLY
LYS
THR
N168
I174
N175
R181
L213
T223
R236
Y245
Y246
H247
C253
R270
ARG
GLN
GLY
C274
K283
M294
I321
Q328
E329
L330
T334
R345
L350
L354
E355
I361
K369
R372
R383
Y401
T422
Q423
H429
L436
I439
H440
A458
Y477
I478
R479
T480
S481
F482
R488
R498
D499
F518
ASP
GLY
GLN
ASP
ALA
CYS
GLY
SER
ASN
S528
R539
P549
R554
P558
W559
T560
Q561
T578
Y579
Y587
T590
D591
A592
T593
N594
P595
S596
V597
P598
L599
V604
I612
L613
P618
S619
D620
P621
N622
I625
V630
R634
Q635
D638
S639
E640
L641
F642
E643
K649
G650
L651
K652
L653
P654
S655
R656
THR
TRP
SER
PRO
PRO
PHE
GLU
SER
GLU
ASP
SER
GLN
LYS
HIS
ASN
GLN
SER
GLU
TYR
GLU
ASP
SER
ALA
GLY
GLU
CYS
CYS
SER
CYS
PRO
LYS
THR
ASP
SER
Q691
E697
K703
E706
H710
V713
F714
R717
PRO
SER
ARG
LYS
ARG
ARG
SER
LEU
GLY
ASP
VAL
GLY
ASN
VAL
THR
VAL
ALA
VAL
PRO
THR
VAL
ALA
ALA
PHE
PRO
ASN
THR
SER
SER
THR
SER
VAL
PRO
THR
SER
PRO
E754
E755
H756
T777
G778
Y779
R780
I781
E782
L783
Q784
A785
T790
P791
E792
S796
V797
A798
R804
E808
A811
I822
V828
H829
L830
M831
W832
P835
K836
E837
P838
L841
I842
Y849
R850
R851
E856
L859
C860
V861
K864
H865
F866
C872
L877
S878
P879
Y882
S883
V884
R885
I886
R887
L891
S896
W897
P900
T901
Y902
F903
Y904
V905
Y908
L909
D910
VAL
PRO
SER
ASN
ILE
ALA
LYS
ILE
ILE
ILE
GLY
PRO
LEU
ILE
PHE
VAL
PHE
LEU
PHE
SER
VAL
VAL
ILE
GLY
SER
ILE
TYR
LEU
PHE
LEU
ARG
LYS
ARG
GLN
PRO
ASP
GLY
PRO
LEU
GLY
PRO
LEU
TYR
ALA
SER
SER
ASN
PRO
GLU
PHE
LEU
THR
ALA
SER
ASP
VAL
PHE
PRO
CYS
SER
VAL
TYR
VAL
PRO
ASP
GLU
TRP
GLU
VAL
SER
ARG
GLU
LYS
ILE
THR
LEU
LEU
ARG
GLU
LEU
GLY
GLN
GLY
SER
PHE
GLY
MET
VAL
TYR
GLU
GLY
ASN
ALA
ARG
ASP
ILE
ILE
LYS
GLY
GLU
ALA
GLU
THR
ARG
VAL
ALA
VAL
LYS
THR
VAL
ASN
GLU
SER
ALA
SER
LEU
ARG
GLU
ARG
ILE
GLU
PHE
LEU
ASN
GLU
ALA
SER
VAL
MET
LYS
GLY
PHE
THR
CYS
HIS
HIS
VAL
VAL
ARG
LEU
LEU
GLY
VAL
VAL
SER
LYS
GLY
GLN
PRO
THR
LEU
VAL
VAL
MET
GLU
LEU
MET
ALA
HIS
GLY
ASP
LEU
LYS
SER
TYR
LEU
ARG
SER
LEU
ARG
PRO
GLU
ALA
GLU
ASN
ASN
PRO
GLY
ARG
PRO
PRO
PRO
THR
LEU
GLN
GLU
MET
ILE
GLN
MET
ALA
ALA
GLU
ILE
ALA
ASP
GLY
MET
ALA
TYR
LEU
ASN
ALA
LYS
LYS
PHE
VAL
HIS
ARG
ASN
LEU
ALA
ALA
ARG
ASN
CYS
MET
VAL
ALA
HIS
ASP
PHE
THR
VAL
LYS
ILE
GLY
ASP
PHE
GLY
MET
THR
ARG
ASP
ILE
TYR
GLU
THR
ASP
TYR
TYR
ARG
LYS
GLY
GLY
LYS
GLY
LEU
LEU
PRO
VAL
ARG
TRP
MET
ALA
PRO
GLU
SER
LEU
LYS
ASP
GLY
VAL
PHE
THR
THR
SER
SER
ASP
MET
TRP
SER
PHE
GLY
VAL
VAL
LEU
TRP
GLU
ILE
THR
SER
LEU
ALA
GLU
GLN
PRO
TYR
GLN
GLY
LEU
SER
ASN
GLU
GLN
VAL
LEU
LYS
PHE
VAL
MET
ASP
GLY
GLY
TYR
LEU
ASP
GLN
PRO
ASP
ASN
CYS
PRO
GLU
ARG
VAL
THR
ASP
LEU
MET
ARG
MET
CYS
TRP
GLN
PHE
ASN
PRO
LYS
MET
ARG
PRO
THR
PHE
LEU
GLU
ILE
VAL
ASN
LEU
LEU
LYS
ASP
ASP
LEU
HIS
PRO
SER
PHE
PRO
GLU
VAL
SER
PHE
PHE
HIS
SER
GLU
GLU
ASN
LYS
ALA
PRO
GLU
SER
GLU
GLU
LEU
GLU
MET
GLU
PHE
GLU
ASP
MET
GLU
ASN
VAL
PRO
LEU
ASP
ARG
SER
SER
HIS
CYS
GLN
ARG
GLU
GLU
ALA
GLY
GLY
ARG
ASP
GLY
GLY
SER
SER
LEU
GLY
PHE
LYS
ARG
SER
TYR
GLU
GLU
HIS
ILE
PRO
TYR
THR
HIS
MET
ASN
GLY
GLY
LYS
LYS
ASN
GLY
ALA
ALA
Page 6 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV
ALA
THR
ALA
PRO
ARG
SER
ASN
PRO
SER
LEU
GLU
SER
SER
GLY
LEU
GLU
VAL
LEU
PHE
GLN
• Molecule 1: Insulin receptor
Chain C:
H1 R14
L20
L23
I29
L49
V99
H100
L101
K102
N111
R114
L125
Y144
I145
V146
L147
E154
T162
ALA
LYS
GLY
LYS
THR
N168
I174
N175
R181
L213
T223
R236
Y245
Y246
H247
C253
R270
ARG
GLN
GLY
C274
K283
M294
I321
Q328
E329
L330
T334
R345
L350
L354
E355
I361
K369
R383
Y401
T422
Q423
H429
L436
I439
H440
A458
Y477
I478
R479
T480
S481
F482
R488
R498
D499
N514
F518
ASP
GLY
GLN
ASP
ALA
CYS
GLY
SER
ASN
S528
R539
P549
R554
P558
W559
T560
Q561
T578
Y579
Y587
T590
D591
A592
T593
N594
P595
S596
V597
P598
L599
V604
I612
L613
P618
S619
D620
P621
N622
I625
V630
R634
Q635
D638
S639
E640
L641
F642
E643
K649
G650
L651
K652
L653
P654
S655
R656
THR
TRP
SER
PRO
PRO
PHE
GLU
SER
GLU
ASP
SER
GLN
LYS
HIS
ASN
GLN
SER
GLU
TYR
GLU
ASP
SER
ALA
GLY
GLU
CYS
CYS
SER
CYS
PRO
LYS
THR
ASP
SER
Q691
E697
K703
E706
H710
V713
F714
R717
PRO
SER
ARG
LYS
ARG
ARG
SER
LEU
GLY
ASP
VAL
GLY
ASN
VAL
THR
VAL
ALA
VAL
PRO
THR
VAL
ALA
ALA
PHE
PRO
ASN
THR
SER
SER
THR
SER
VAL
PRO
THR
SER
PRO
E754
E755
H756
T777
G778
Y779
R780
I781
E782
L783
Q784
A785
T790
P791
E792
S796
V797
A798
R804
E808
A811
I822
V828
H829
L830
M831
W832
P835
K836
E837
P838
L841
I842
Y849
R850
R851
E856
L859
C860
V861
K864
H865
F866
C872
L877
S878
P879
Y882
S883
V884
R885
I886
R887
L891
S896
W897
P900
T901
Y902
F903
Y904
V905
Y908
L909
D910
VAL
PRO
SER
ASN
ILE
ALA
LYS
ILE
ILE
ILE
GLY
PRO
LEU
ILE
PHE
VAL
PHE
LEU
PHE
SER
VAL
VAL
ILE
GLY
SER
ILE
TYR
LEU
PHE
LEU
ARG
LYS
ARG
GLN
PRO
ASP
GLY
PRO
LEU
GLY
PRO
LEU
TYR
ALA
SER
SER
ASN
PRO
GLU
PHE
LEU
THR
ALA
SER
ASP
VAL
PHE
PRO
CYS
SER
VAL
TYR
VAL
PRO
ASP
GLU
TRP
GLU
VAL
SER
ARG
GLU
LYS
ILE
THR
LEU
LEU
ARG
GLU
LEU
GLY
GLN
GLY
SER
PHE
GLY
MET
VAL
TYR
GLU
GLY
ASN
ALA
ARG
ASP
ILE
ILE
LYS
GLY
GLU
ALA
GLU
THR
ARG
VAL
ALA
VAL
LYS
THR
VAL
ASN
GLU
SER
ALA
SER
LEU
ARG
GLU
ARG
ILE
GLU
PHE
LEU
ASN
GLU
ALA
SER
VAL
MET
LYS
GLY
PHE
THR
CYS
HIS
HIS
VAL
VAL
ARG
LEU
LEU
GLY
VAL
VAL
SER
LYS
GLY
GLN
PRO
THR
LEU
VAL
VAL
MET
GLU
LEU
MET
ALA
HIS
GLY
ASP
LEU
LYS
SER
TYR
LEU
ARG
SER
LEU
ARG
PRO
GLU
ALA
GLU
ASN
ASN
PRO
GLY
ARG
PRO
PRO
PRO
THR
LEU
GLN
GLU
MET
ILE
GLN
MET
ALA
ALA
GLU
ILE
ALA
ASP
GLY
MET
ALA
TYR
LEU
ASN
ALA
LYS
LYS
PHE
VAL
HIS
ARG
ASN
LEU
ALA
ALA
ARG
ASN
CYS
MET
VAL
ALA
HIS
ASP
PHE
THR
VAL
LYS
ILE
GLY
ASP
PHE
GLY
MET
THR
ARG
ASP
ILE
TYR
GLU
THR
ASP
TYR
TYR
ARG
LYS
GLY
GLY
LYS
GLY
LEU
LEU
PRO
VAL
ARG
TRP
MET
ALA
PRO
GLU
SER
LEU
LYS
ASP
GLY
VAL
PHE
THR
THR
SER
SER
ASP
MET
TRP
SER
PHE
GLY
VAL
VAL
LEU
TRP
GLU
ILE
THR
SER
LEU
ALA
GLU
GLN
PRO
TYR
GLN
GLY
LEU
SER
ASN
GLU
GLN
VAL
LEU
LYS
PHE
VAL
MET
ASP
GLY
GLY
TYR
LEU
ASP
GLN
PRO
ASP
ASN
CYS
PRO
GLU
ARG
VAL
THR
ASP
LEU
MET
ARG
MET
CYS
TRP
GLN
PHE
ASN
PRO
LYS
MET
ARG
PRO
THR
PHE
LEU
GLU
ILE
VAL
ASN
LEU
LEU
LYS
ASP
ASP
LEU
HIS
PRO
SER
PHE
PRO
GLU
VAL
SER
PHE
PHE
HIS
SER
GLU
GLU
ASN
LYS
ALA
PRO
GLU
SER
GLU
GLU
LEU
GLU
MET
GLU
PHE
GLU
ASP
MET
GLU
ASN
VAL
PRO
LEU
ASP
ARG
SER
SER
HIS
CYS
GLN
ARG
GLU
GLU
ALA
GLY
GLY
ARG
ASP
GLY
GLY
SER
SER
LEU
GLY
PHE
LYS
ARG
SER
TYR
GLU
GLU
HIS
ILE
PRO
TYR
THR
HIS
MET
ASN
GLY
GLY
LYS
LYS
ASN
GLY
ALA
ALA
ALA
THR
ALA
PRO
ARG
SER
ASN
PRO
SER
LEU
GLU
SER
SER
GLY
LEU
GLU
VAL
LEU
PHE
GLN
• Molecule 2: Insulin
Chain D:
Page 7 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV
PHE
V2 C19
G20
E21
R22
G23
F24
F25
Y26
T27
P28
LYS
THR
ARG
ARG
GLU
ALA
GLU
ASP
LEU
GLN
GLY
SER
LEU
GLN
PRO
LEU
ALA
LEU
GLU
GLY
SER
LEU
GLN
LYS
ARG
G56
S67
Q70
N76
• Molecule 2: Insulin
Chain E:
PHE
V2 C19
G20
E21
R22
Y26
T27
P28
LYS
THR
ARG
ARG
GLU
ALA
GLU
ASP
LEU
GLN
GLY
SER
LEU
GLN
PRO
LEU
ALA
LEU
GLU
GLY
SER
LEU
GLN
LYS
ARG
G56
S67
Q70
N76
• Molecule 2: Insulin
Chain F:
PHE
VAL
ASN
Q4 C7 H10
L17
V18
C19
G20
E21
R22
G23
F24
F25
Y26
THR
PRO
LYS
THR
ARG
ARG
GLU
ALA
GLU
ASP
LEU
GLN
GLY
SER
LEU
GLN
PRO
LEU
ALA
LEU
GLU
GLY
SER
LEU
GLN
LYS
ARG
G56
S67
L68
Y69
Q70
N76
• Molecule 2: Insulin
Chain G:
PHE
VAL
ASN
Q4 L17
V18
C19
G20
E21
R22
Y26
THR
PRO
LYS
THR
ARG
ARG
GLU
ALA
GLU
ASP
LEU
GLN
GLY
SER
LEU
GLN
PRO
LEU
ALA
LEU
GLU
GLY
SER
LEU
GLN
LYS
ARG
G56
S67
L68
Y69
Q70
N76
Page 8 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV
4 Experimental information i○
Property Value SourceReconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C2 DepositorNumber of particles used 235707 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
) 50 DepositorMinimum defocus (nm) Not provided DepositorMaximum defocus (nm) Not provided DepositorMagnification Not provided DepositorImage detector GATAN K2 IS (4k x 4k) Depositor
Page 9 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV
5 Model quality i○
5.1 Standard geometry i○
The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
Mol Chain Bond lengths Bond anglesRMSZ #|Z| >2 RMSZ #|Z| >2
1 A 0.46 0/6828 0.69 0/92581 C 0.46 0/6828 0.70 0/92582 D 0.35 0/383 0.51 0/5182 E 0.35 0/383 0.51 0/5182 F 0.37 0/353 0.54 0/4752 G 0.37 0/353 0.54 0/475All All 0.45 0/15128 0.68 0/20502
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 C 0 1All All 0 2
There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
All (2) planarity outliers are listed below:
Mol Chain Res Type Group1 A 578 THR Peptide1 C 578 THR 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 hydrogen
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atoms 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 6664 0 6478 108 01 C 6664 0 6478 114 02 D 376 0 346 5 02 E 376 0 346 4 02 F 347 0 317 8 02 G 347 0 317 9 0All All 14774 0 14282 232 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 8.
All (232) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:482:PHE:CZ 1:C:593:THR:HG21 1.45 1.501:A:482:PHE:CZ 1:A:593:THR:HG21 1.58 1.361:A:482:PHE:CE1 1:A:593:THR:HB 1.60 1.331:C:482:PHE:CZ 1:C:593:THR:CG2 2.13 1.301:C:482:PHE:CE1 1:C:593:THR:CG2 2.14 1.301:A:482:PHE:HE1 1:A:593:THR:CB 1.45 1.281:C:482:PHE:CE1 1:C:593:THR:HB 1.74 1.231:C:482:PHE:HE1 1:C:593:THR:CB 1.52 1.211:A:559:TRP:HB2 1:A:592:ALA:HB2 1.25 1.141:C:482:PHE:CE1 1:C:593:THR:CB 2.29 1.121:A:482:PHE:CZ 1:A:593:THR:CG2 2.34 1.101:C:559:TRP:HB2 1:C:592:ALA:HB2 1.17 1.101:A:482:PHE:CE1 1:A:593:THR:CB 2.26 1.091:A:482:PHE:CE1 1:A:593:THR:CG2 2.35 1.081:A:559:TRP:HB2 1:A:592:ALA:CB 1.88 1.031:A:482:PHE:HZ 1:A:593:THR:HG21 0.91 1.021:C:482:PHE:HE1 1:C:593:THR:HB 1.06 0.971:A:482:PHE:HE1 1:A:593:THR:HB 0.80 0.941:C:482:PHE:CE1 1:C:593:THR:HG22 2.02 0.931:A:559:TRP:CB 1:A:592:ALA:HB2 2.04 0.881:C:482:PHE:HZ 1:C:593:THR:CG2 1.66 0.861:A:790:THR:HB 1:A:791:PRO:HD3 1.57 0.861:C:790:THR:HB 1:C:791:PRO:HD3 1.57 0.851:C:482:PHE:HE1 1:C:593:THR:CG2 1.69 0.851:C:482:PHE:HZ 1:C:593:THR:HG21 0.88 0.81
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:559:TRP:HB2 1:C:592:ALA:CB 2.07 0.781:A:755:GLU:HG2 1:A:756:HIS:N 1.99 0.761:A:755:GLU:HG2 1:A:756:HIS:H 1.51 0.751:C:755:GLU:HG2 1:C:756:HIS:N 1.99 0.751:C:350:LEU:O 1:C:354:LEU:HB2 1.88 0.741:A:350:LEU:O 1:A:354:LEU:HB2 1.88 0.72
1:C:755:GLU:HG2 1:C:756:HIS:H 1.51 0.721:C:599:LEU:HD11 1:C:619:SER:HB3 1.72 0.721:A:599:LEU:HD11 1:A:619:SER:HB3 1.72 0.721:A:885:ARG:HE 1:A:897:TRP:HB3 1.56 0.701:C:885:ARG:HE 1:C:897:TRP:HB3 1.56 0.691:A:590:THR:OG1 1:A:591:ASP:N 2.27 0.681:C:482:PHE:CZ 1:C:593:THR:HG22 2.14 0.671:C:590:THR:OG1 1:C:591:ASP:N 2.27 0.671:C:785:ALA:H 1:C:796:SER:HB3 1.60 0.66
1:A:651:LEU:HD23 1:A:651:LEU:H 1.62 0.641:A:785:ALA:H 1:A:796:SER:HB3 1.60 0.64
1:A:597:VAL:HG22 1:A:797:VAL:CG2 2.28 0.641:C:651:LEU:H 1:C:651:LEU:HD23 1.62 0.63
1:A:808:GLU:HB2 1:A:811:ALA:HB2 1.80 0.631:C:808:GLU:HB2 1:C:811:ALA:HB2 1.81 0.631:C:597:VAL:HG22 1:C:797:VAL:CG2 2.28 0.621:C:559:TRP:CB 1:C:592:ALA:HB2 2.10 0.621:C:879:PRO:HA 1:C:905:VAL:HG23 1.82 0.611:A:879:PRO:HA 1:A:905:VAL:HG23 1.82 0.61
1:C:223:THR:HG22 1:C:236:ARG:HG2 1.82 0.611:A:643:GLU:HA 1:A:864:LYS:HE3 1.82 0.60
1:A:223:THR:HG22 1:A:236:ARG:HG2 1.82 0.601:C:643:GLU:HA 1:C:864:LYS:HE3 1.82 0.601:C:593:THR:O 1:C:594:ASN:O 2.20 0.59
1:A:558:PRO:HB3 1:A:592:ALA:HA 1.84 0.591:C:422:THR:HG22 1:C:423:GLN:HG3 1.86 0.571:C:822:ILE:HG12 1:C:828:VAL:HG22 1.86 0.571:C:482:PHE:HA 1:C:591:ASP:OD1 2.05 0.571:A:634:ARG:HD2 1:A:777:THR:HG21 1.87 0.561:A:422:THR:HG22 1:A:423:GLN:HG3 1.86 0.561:A:593:THR:O 1:A:622:ASN:HB2 2.05 0.56
1:A:822:ILE:HG12 1:A:828:VAL:HG22 1.86 0.561:C:634:ARG:HD2 1:C:777:THR:HG21 1.87 0.561:C:885:ARG:NH1 1:C:900:PRO:HD3 2.21 0.561:A:604:VAL:HB 1:A:612:ILE:HG13 1.88 0.56
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:835:PRO:HD2 1:A:842:ILE:HD12 1.88 0.561:C:835:PRO:HD2 1:C:842:ILE:HD12 1.88 0.551:A:885:ARG:NH1 1:A:900:PRO:HD3 2.21 0.551:C:558:PRO:HB3 1:C:592:ALA:HA 1.88 0.551:C:499:ASP:OD1 1:C:703:LYS:NZ 2.37 0.551:C:604:VAL:HB 1:C:612:ILE:HG13 1.88 0.551:C:436:LEU:O 1:C:440:HIS:ND1 2.34 0.531:A:482:PHE:HA 1:A:591:ASP:OD1 2.08 0.531:A:593:THR:O 1:A:594:ASN:O 2.25 0.53
1:C:613:LEU:HD22 1:C:781:ILE:HG21 1.91 0.531:C:479:ARG:NH2 2:F:17:LEU:O 2.41 0.531:A:477:TYR:HB3 1:A:488:ARG:HB2 1.92 0.521:C:355:GLU:OE2 1:C:383:ARG:NH2 2.33 0.521:C:477:TYR:HB3 1:C:488:ARG:HB2 1.92 0.521:A:479:ARG:NH2 2:G:17:LEU:O 2.42 0.521:A:436:LEU:O 1:A:440:HIS:ND1 2.34 0.52
1:A:613:LEU:HD22 1:A:781:ILE:HG21 1.91 0.521:C:593:THR:O 1:C:622:ASN:HB2 2.10 0.522:F:67:SER:OG 2:F:70:GLN:NE2 2.43 0.52
1:A:654:PRO:HG2 1:A:656:ARG:HH21 1.73 0.521:A:499:ASP:OD1 1:A:703:LYS:NZ 2.36 0.521:C:654:PRO:HG2 1:C:656:ARG:HH21 1.73 0.521:A:355:GLU:OE2 1:A:383:ARG:NH2 2.33 0.512:D:67:SER:OG 2:D:70:GLN:NE2 2.43 0.512:G:67:SER:OG 2:G:70:GLN:NE2 2.43 0.511:A:482:PHE:CE1 1:A:593:THR:HG22 2.41 0.511:A:597:VAL:HG22 1:A:797:VAL:HG23 1.92 0.511:C:154:GLU:OE2 2:G:56:GLY:N 2.44 0.511:C:597:VAL:HG22 1:C:797:VAL:HG23 1.92 0.511:A:23:LEU:HD11 1:A:29:ILE:HD11 1.93 0.511:A:247:HIS:HB2 1:A:283:LYS:HG2 1.93 0.501:A:635:GLN:HE21 1:A:780:ARG:HB2 1.76 0.502:E:67:SER:OG 2:E:70:GLN:NE2 2.43 0.50
1:A:597:VAL:HG22 1:A:797:VAL:HG22 1.93 0.501:A:144:TYR:CE2 1:A:146:VAL:HG12 2.46 0.501:C:597:VAL:HG22 1:C:797:VAL:HG22 1.93 0.501:A:488:ARG:HE 2:G:68:LEU:HD21 1.77 0.501:A:630:VAL:HG22 1:A:783:LEU:HD13 1.94 0.501:C:482:PHE:CE1 1:C:593:THR:HG21 1.97 0.501:A:144:TYR:CE2 1:A:146:VAL:CG1 2.95 0.491:C:247:HIS:HB2 1:C:283:LYS:HG2 1.93 0.49
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:635:GLN:HE21 1:C:780:ARG:HB2 1.76 0.491:C:23:LEU:HD11 1:C:29:ILE:HD11 1.93 0.491:C:111:ASN:HD22 1:C:213:LEU:HD11 1.76 0.491:C:630:VAL:HG22 1:C:783:LEU:HD13 1.94 0.491:A:436:LEU:HD23 1:A:439:ILE:HD12 1.95 0.481:A:114:ARG:HH22 1:A:328:GLN:HE21 1.60 0.481:A:111:ASN:HD22 1:A:213:LEU:HD11 1.76 0.48
1:A:1:HIS:N 1:A:223:THR:O 2.37 0.481:A:877:LEU:N 1:A:877:LEU:HD12 2.29 0.48
1:C:114:ARG:HH22 1:C:328:GLN:HE21 1.60 0.481:A:481:SER:HB2 2:G:17:LEU:HD21 1.96 0.481:C:436:LEU:HD23 1:C:439:ILE:HD12 1.95 0.481:C:481:SER:HB2 2:F:17:LEU:HD21 1.96 0.481:A:593:THR:O 1:A:594:ASN:C 2.51 0.48
1:C:782:GLU:HG3 1:C:798:ALA:HB1 1.96 0.471:A:830:LEU:HB2 1:A:872:CYS:HB3 1.96 0.471:C:144:TYR:CE2 1:C:146:VAL:HG12 2.49 0.47
1:C:1:HIS:N 1:C:223:THR:O 2.37 0.472:E:67:SER:H 2:E:70:GLN:HE21 1.61 0.47
1:C:851:ARG:HB2 1:C:882:TYR:CE2 2.49 0.471:A:14:ARG:NH2 1:C:713:VAL:O 2.35 0.472:F:67:SER:H 2:F:70:GLN:HE21 1.61 0.47
1:A:559:TRP:HB2 1:A:592:ALA:HB3 1.88 0.471:A:481:SER:O 1:A:591:ASP:OD1 2.33 0.47
1:A:782:GLU:HG3 1:A:798:ALA:HB1 1.97 0.471:A:851:ARG:HB2 1:A:882:TYR:CE2 2.49 0.471:A:345:ARG:NH1 1:C:697:GLU:OE1 2.46 0.471:C:877:LEU:HD12 1:C:877:LEU:N 2.29 0.47
2:G:67:SER:H 2:G:70:GLN:HE21 1.61 0.472:D:67:SER:H 2:D:70:GLN:HE21 1.61 0.47
1:C:859:LEU:HD23 1:C:872:CYS:SG 2.55 0.472:E:19:CYS:SG 2:E:22:ARG:NH2 2.88 0.462:G:19:CYS:SG 2:G:22:ARG:NH2 2.88 0.461:A:706:GLU:O 1:A:710:HIS:ND1 2.45 0.462:D:19:CYS:SG 2:D:22:ARG:NH2 2.88 0.46
1:C:830:LEU:HB2 1:C:872:CYS:HB3 1.96 0.462:F:19:CYS:SG 2:F:22:ARG:NH2 2.88 0.461:C:334:THR:HA 1:C:361:ILE:HA 1.97 0.461:A:621:PRO:HB3 1:A:625:ILE:HD11 1.98 0.461:C:144:TYR:CE2 1:C:146:VAL:CG1 2.98 0.461:A:697:GLU:OE1 1:C:345:ARG:NH1 2.46 0.46
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:477:TYR:OH 2:G:21:GLU:OE2 2.34 0.461:C:481:SER:O 1:C:591:ASP:OD1 2.34 0.461:C:593:THR:O 1:C:594:ASN:C 2.54 0.46
1:C:885:ARG:HH12 1:C:900:PRO:HD3 1.81 0.461:C:498:ARG:NH1 1:C:706:GLU:OE1 2.48 0.451:A:334:THR:HA 1:A:361:ILE:HA 1.97 0.451:A:859:LEU:HD23 1:A:872:CYS:SG 2.55 0.451:C:706:GLU:O 1:C:710:HIS:ND1 2.45 0.452:F:24:PHE:CD2 2:F:26:TYR:HB2 2.51 0.452:G:26:TYR:CD1 2:G:26:TYR:C 2.90 0.45
1:A:885:ARG:HH12 1:A:900:PRO:HD3 1.81 0.451:C:621:PRO:HB3 1:C:625:ILE:HD11 1.98 0.451:C:828:VAL:HG21 1:C:903:PHE:CE1 2.51 0.451:A:713:VAL:O 1:C:14:ARG:NH2 2.35 0.45
1:A:861:VAL:HG12 1:A:866:PHE:HB2 1.99 0.451:A:828:VAL:HG21 1:A:903:PHE:CE1 2.52 0.441:C:369:LYS:HG3 1:C:401:TYR:HB3 1.99 0.441:A:498:ARG:NH1 1:A:706:GLU:OE1 2.48 0.441:A:369:LYS:HG3 1:A:401:TYR:HB3 1.99 0.441:C:832:TRP:HH2 1:C:872:CYS:HB2 1.82 0.441:A:832:TRP:HH2 1:A:872:CYS:HB2 1.82 0.441:A:849:TYR:HA 1:A:883:SER:O 2.17 0.441:C:755:GLU:CG 1:C:756:HIS:H 2.27 0.441:A:640:GLU:CD 1:A:640:GLU:H 2.21 0.441:A:641:LEU:HB3 1:A:841:LEU:HD21 1.99 0.44
2:F:7:CYS:O 2:F:10:HIS:HB2 2.18 0.441:C:641:LEU:HB3 1:C:841:LEU:HD21 1.99 0.441:C:850:ARG:NH2 1:C:856:GLU:HB2 2.33 0.431:C:849:TYR:HA 1:C:883:SER:O 2.17 0.431:C:861:VAL:HG12 1:C:866:PHE:HB2 1.99 0.431:C:102:LYS:HA 1:C:125:LEU:HA 2.00 0.431:A:651:LEU:CD2 1:A:651:LEU:H 2.30 0.431:A:710:HIS:HD2 1:A:714:PHE:HE2 1.66 0.431:A:144:TYR:HE2 1:A:146:VAL:HG12 1.83 0.431:C:429:HIS:CE1 1:C:458:ALA:HB2 2.54 0.431:A:832:TRP:CH2 1:A:872:CYS:HB2 2.54 0.431:A:850:ARG:NH2 1:A:856:GLU:HB2 2.33 0.431:C:640:GLU:H 1:C:640:GLU:CD 2.21 0.43
1:A:596:SER:HB3 1:A:618:PRO:HB2 2.01 0.431:C:778:GLY:HA2 1:C:804:ARG:HA 2.01 0.431:C:832:TRP:CH2 1:C:872:CYS:HB2 2.54 0.43
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:174:ILE:HB 1:A:181:ARG:HH22 1.84 0.431:C:596:SER:HB3 1:C:618:PRO:HB2 2.01 0.421:C:710:HIS:HD2 1:C:714:PHE:HE2 1.66 0.421:C:790:THR:HB 1:C:791:PRO:CD 2.40 0.421:A:654:PRO:HB2 1:A:656:ARG:HE 1.84 0.421:C:593:THR:O 1:C:622:ASN:CB 2.67 0.421:A:429:HIS:CE1 1:A:458:ALA:HB2 2.54 0.421:C:14:ARG:CZ 2:E:26:TYR:HB2 2.49 0.42
1:A:245:TYR:HB3 1:A:253:CYS:HB3 2.01 0.421:C:653:LEU:HD21 1:C:891:LEU:HD23 2.01 0.421:A:102:LYS:HA 1:A:125:LEU:HA 2.01 0.421:C:654:PRO:HB2 1:C:656:ARG:HE 1.84 0.421:A:561:GLN:HE21 1:A:587:TYR:HB3 1.85 0.421:A:778:GLY:HA2 1:A:804:ARG:HA 2.01 0.421:C:321:ILE:HD11 1:C:330:LEU:HD12 2.01 0.421:A:593:THR:O 1:A:622:ASN:CB 2.67 0.41
1:A:653:LEU:HD21 1:A:891:LEU:HD23 2.01 0.411:C:147:LEU:HD23 1:C:147:LEU:HA 1.93 0.411:C:558:PRO:CB 1:C:592:ALA:HA 2.50 0.411:C:514:ASN:OD1 1:C:514:ASN:N 2.51 0.411:C:174:ILE:HB 1:C:181:ARG:HH22 1.84 0.41
1:C:245:TYR:HB3 1:C:253:CYS:HB3 2.01 0.411:C:488:ARG:HE 2:F:68:LEU:HD21 1.84 0.411:A:15:ASN:HD21 2:D:24:PHE:H 1.68 0.411:C:887:ARG:HB2 1:C:897:TRP:CD2 2.56 0.411:A:321:ILE:HD11 1:A:330:LEU:HD12 2.01 0.411:C:561:GLN:HE21 1:C:587:TYR:HB3 1.85 0.411:C:598:PRO:HG2 1:C:783:LEU:HG 2.03 0.411:A:14:ARG:CZ 2:D:26:TYR:HB2 2.51 0.411:A:121:LYS:NZ 1:C:706:GLU:OE2 2.44 0.411:A:885:ARG:HE 1:A:897:TRP:CB 2.29 0.411:A:887:ARG:HB2 1:A:897:TRP:CD2 2.56 0.411:C:350:LEU:O 1:C:354:LEU:CB 2.65 0.41
1:A:345:ARG:HH21 1:A:372:ARG:HD2 1.86 0.411:C:99:VAL:HG12 1:C:100:HIS:CD2 2.56 0.411:C:597:VAL:HA 1:C:796:SER:HG 1.86 0.411:A:882:TYR:O 1:A:902:TYR:HA 2.21 0.40
1:A:20:LEU:HD23 1:A:49:LEU:HD21 2.03 0.401:C:755:GLU:CG 1:C:756:HIS:N 2.77 0.401:A:99:VAL:HG12 1:A:100:HIS:CD2 2.56 0.401:C:882:TYR:O 1:C:902:TYR:HA 2.21 0.40
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:144:TYR:HE2 1:A:146:VAL:CG1 2.33 0.401:C:20:LEU:HD23 1:C:49:LEU:HD21 2.03 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 811/1354 (60%) 719 (89%) 80 (10%) 12 (2%) 11 49
1 C 811/1354 (60%) 719 (89%) 79 (10%) 13 (2%) 11 47
2 D 44/74 (60%) 41 (93%) 2 (4%) 1 (2%) 7 38
2 E 44/74 (60%) 41 (93%) 2 (4%) 1 (2%) 7 38
2 F 40/74 (54%) 37 (92%) 2 (5%) 1 (2%) 6 36
2 G 40/74 (54%) 37 (92%) 2 (5%) 1 (2%) 6 36
All All 1790/3004 (60%) 1594 (89%) 167 (9%) 29 (2%) 15 47
All (29) Ramachandran outliers are listed below:
Mol Chain Res Type1 A 649 LYS1 A 790 THR1 A 896 SER1 C 649 LYS1 C 790 THR1 C 896 SER1 A 579 TYR1 A 638 ASP1 C 579 TYR1 C 594 ASN
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Continued from previous page...Mol Chain Res Type1 C 638 ASP1 A 650 GLY1 C 650 GLY1 A 594 ASN1 A 792 GLU1 C 792 GLU1 A 836 LYS1 A 908 TYR1 C 590 THR1 C 836 LYS1 C 908 TYR1 A 838 PRO1 C 838 PRO1 A 549 PRO2 D 20 GLY2 E 20 GLY2 F 20 GLY2 G 20 GLY1 C 549 PRO
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 751/1209 (62%) 744 (99%) 7 (1%) 81 93
1 C 751/1209 (62%) 744 (99%) 7 (1%) 81 93
2 D 43/65 (66%) 43 (100%) 0 100 100
2 E 43/65 (66%) 43 (100%) 0 100 100
2 F 39/65 (60%) 39 (100%) 0 100 100
2 G 39/65 (60%) 39 (100%) 0 100 100
All All 1666/2678 (62%) 1652 (99%) 14 (1%) 84 94
All (14) residues with a non-rotameric sidechain are listed below:
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Mol Chain Res Type1 A 175 ASN1 A 270 ARG1 A 294 MET1 A 539 ARG1 A 554 ARG1 A 638 ASP1 A 651 LEU1 C 175 ASN1 C 270 ARG1 C 294 MET1 C 539 ARG1 C 554 ARG1 C 638 ASP1 C 651 LEU
Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (27) suchsidechains are listed below:
Mol Chain Res Type1 A 15 ASN1 A 32 HIS1 A 34 GLN1 A 100 HIS1 A 175 ASN1 A 209 HIS1 A 546 GLN1 A 561 GLN1 A 610 GLN1 A 635 GLN1 C 15 ASN1 C 32 HIS1 C 34 GLN1 C 100 HIS1 C 175 ASN1 C 209 HIS1 C 546 GLN1 C 561 GLN1 C 610 GLN1 C 635 GLN2 D 3 ASN2 D 70 GLN2 E 3 ASN2 E 10 HIS2 E 70 GLN
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Page 19 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV
Continued from previous page...Mol Chain Res Type2 F 70 GLN2 G 70 GLN
5.3.3 RNA i○
There are no RNA molecules in this entry.
5.4 Non-standard residues in protein, DNA, RNA chains i○
There are no non-standard protein/DNA/RNA residues in this entry.
5.5 Carbohydrates i○
There are no carbohydrates in this entry.
5.6 Ligand geometry i○
There are no ligands in this entry.
5.7 Other polymers i○
There are no such residues in this entry.
5.8 Polymer linkage issues i○
There are no chain breaks in this entry.