Full wwPDB EM Model Validation Report i · 2020-03-03 · Page3 FullwwPDBEMModelValidationReport...
Transcript of Full wwPDB EM Model Validation Report i · 2020-03-03 · Page3 FullwwPDBEMModelValidationReport...
Full wwPDB EM Model Validation Report i○
Mar 3, 2020 – 11:47 AM EST
PDB ID : 6M18EMDB ID : EMD-30040
Title : ACE2-B0AT1 complexAuthors : Yan, R.H.; Zhang, Y.Y.; Li, Y.N.; Xia, L.; Zhou, Q.
Deposited on : 2020-02-25Resolution : 2.90 Å(reported)
This is a Full wwPDB EM Model Validation Report for 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.
The following versions of software and data (see references i○) were used in the production of this report:
MolProbity : 4.02b-467Mogul : 1.8.0 (224370), CSD as540be (2019)
buster-report : 1.1.7 (2018)Percentile 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) : 2.8
Page 2 Full wwPDB EM Model Validation Report 6M18
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 2.90 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 and theirfit 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.A grey segment represents the fraction of residues that are not modelled. The numeric valuefor each fraction is indicated below the corresponding segment, with a dot representing fractions<=5%
Mol Chain Length Quality of chain
1 A 654
1 C 654
2 B 814
2 D 814
Page 3 Full wwPDB EM Model Validation Report 6M18
2 Entry composition i○
There are 6 unique types of molecules in this entry. The entry contains 22534 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 Sodium-dependent neutral amino acid transporter B(0)AT1.
Mol Chain Residues Atoms AltConf Trace
1 A 605 Total C N O S4794 3169 744 851 30 0 0
1 C 605 Total C N O S4794 3169 744 851 30 0 0
There are 42 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA -19 MET - initiating methionine UNP Q695T7A -18 ALA - expression tag UNP Q695T7A -17 ASP - expression tag UNP Q695T7A -16 TYR - expression tag UNP Q695T7A -15 LYS - expression tag UNP Q695T7A -14 ASP - expression tag UNP Q695T7A -13 ASP - expression tag UNP Q695T7A -12 ASP - expression tag UNP Q695T7A -11 ASP - expression tag UNP Q695T7A -10 LYS - expression tag UNP Q695T7A -9 SER - expression tag UNP Q695T7A -8 GLY - expression tag UNP Q695T7A -7 PRO - expression tag UNP Q695T7A -6 ASP - expression tag UNP Q695T7A -5 GLU - expression tag UNP Q695T7A -4 VAL - expression tag UNP Q695T7A -3 ASP - expression tag UNP Q695T7A -2 ALA - expression tag UNP Q695T7A -1 SER - expression tag UNP Q695T7A 0 GLY - expression tag UNP Q695T7A 1 ARG - expression tag UNP Q695T7C -19 MET - initiating methionine UNP Q695T7C -18 ALA - expression tag UNP Q695T7C -17 ASP - expression tag UNP Q695T7C -16 TYR - expression tag UNP Q695T7C -15 LYS - expression tag UNP Q695T7
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Page 4 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Chain Residue Modelled Actual Comment Reference
C -14 ASP - expression tag UNP Q695T7C -13 ASP - expression tag UNP Q695T7C -12 ASP - expression tag UNP Q695T7C -11 ASP - expression tag UNP Q695T7C -10 LYS - expression tag UNP Q695T7C -9 SER - expression tag UNP Q695T7C -8 GLY - expression tag UNP Q695T7C -7 PRO - expression tag UNP Q695T7C -6 ASP - expression tag UNP Q695T7C -5 GLU - expression tag UNP Q695T7C -4 VAL - expression tag UNP Q695T7C -3 ASP - expression tag UNP Q695T7C -2 ALA - expression tag UNP Q695T7C -1 SER - expression tag UNP Q695T7C 0 GLY - expression tag UNP Q695T7C 1 ARG - expression tag UNP Q695T7
• Molecule 2 is a protein called Angiotensin-converting enzyme 2.
Mol Chain Residues Atoms AltConf Trace
2 B 749 Total C N O S6095 3910 1018 1133 34 0 0
2 D 749 Total C N O S6095 3910 1018 1133 34 0 0
There are 20 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceB -8 MET - initiating methionine UNP Q9BYF1B -7 ARG - expression tag UNP Q9BYF1B 10 TRP - insertion UNP Q9BYF1B 11 SER - insertion UNP Q9BYF1B 12 HIS - insertion UNP Q9BYF1B 13 PRO - insertion UNP Q9BYF1B 14 GLN - insertion UNP Q9BYF1B 15 PHE - insertion UNP Q9BYF1B 16 GLU - insertion UNP Q9BYF1B 17 LYS - insertion UNP Q9BYF1D -8 MET - initiating methionine UNP Q9BYF1D -7 ARG - expression tag UNP Q9BYF1D 10 TRP - insertion UNP Q9BYF1D 11 SER - insertion UNP Q9BYF1
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Page 5 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Chain Residue Modelled Actual Comment Reference
D 12 HIS - insertion UNP Q9BYF1D 13 PRO - insertion UNP Q9BYF1D 14 GLN - insertion UNP Q9BYF1D 15 PHE - insertion UNP Q9BYF1D 16 GLU - insertion UNP Q9BYF1D 17 LYS - insertion UNP Q9BYF1
• Molecule 3 is N-ACETYL-D-GLUCOSAMINE (three-letter code: NAG) (formula: C8H15NO6).
Mol Chain Residues Atoms AltConf
3 A 1 Total C N O84 48 6 30 0
3 A 1 Total C N O84 48 6 30 0
3 A 1 Total C N O84 48 6 30 0
3 A 1 Total C N O84 48 6 30 0
3 A 1 Total C N O84 48 6 30 0
3 A 1 Total C N O84 48 6 30 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
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Page 6 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Mol Chain Residues Atoms AltConf
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 B 1 Total C N O182 104 13 65 0
3 C 1 Total C N O84 48 6 30 0
3 C 1 Total C N O84 48 6 30 0
3 C 1 Total C N O84 48 6 30 0
3 C 1 Total C N O84 48 6 30 0
3 C 1 Total C N O84 48 6 30 0
3 C 1 Total C N O84 48 6 30 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
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Page 7 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Mol Chain Residues Atoms AltConf
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
3 D 1 Total C N O182 104 13 65 0
• Molecule 4 is 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE (three-letter code: 3PH)(formula: C39H77O8P).
Mol Chain Residues Atoms AltConf
4 A 1 Total C O P96 78 16 2 0
4 A 1 Total C O P96 78 16 2 0
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Page 8 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Mol Chain Residues Atoms AltConf
4 C 1 Total C O P96 78 16 2 0
4 C 1 Total C O P96 78 16 2 0
• Molecule 5 is ZINC ION (three-letter code: ZN) (formula: Zn).
Mol Chain Residues Atoms AltConf
5 B 1 Total Zn1 1 0
5 D 1 Total Zn1 1 0
• Molecule 6 is water.
Mol Chain Residues Atoms AltConf
6 A 10 Total O10 10 0
6 B 5 Total O5 5 0
6 C 10 Total O10 10 0
6 D 5 Total O5 5 0
Page 9 Full wwPDB EM Model Validation Report 6M18
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: Sodium-dependent neutral amino acid transporter B(0)AT1
Chain A:
MET
ALA
ASP
TYR
LYS
ASP
ASP
ASP
ASP
LYS
SER
GLY
PRO
ASP
GLU
VAL
ASP
ALA
SER
GLY
ARG
VAL
ARG
LEU
V5 L6 P7 N8 R14
S17
L18
A19
E20
L21
E22
T23
I24
E25
Q26
E27
E28
R32
K38
G51
L52
G53
W56
R57
L75
I76
L77
L78
V79
L80
E81
G82
I83
P84
L85
R97
S105
L111
K112
G113
L114
L120
Y129
L181
N182
I183
W205
S206
I213
T219
V223
Y224
I225
T226
L229
P230
Y231
V232
V233
L234
T235
I236
F237
L238
E261
L262
A263
Q264
W268
Q274
S278
F289
S290
S291
V295
H296
N297
S307
V317
Q331
R332
Y333
D334
D335
C336
F337
I341
L350
P351
N354
V355
T356
Q357
E358
V361
Q364
C383
F388
V393
L398
V402
K409
L427
S430
M436
E437
G438
V439
V440
V441
P442
L443
L461
I462
C463
L464
G465
T466
I497
M502
V508
V511
F520
H524
W530
R535
K572
S573
Y583
V584
V585
V586
V587
I588
V589
A590
G591
V592
P593
S594
L595
T596
I597
P598
G599
Y600
K604
L605
H609
CYS
GLN
LYS
PRO
GLY
ASP
HIS
GLN
GLY
LEU
VAL
SER
THR
LEU
SER
THR
ALA
SER
MET
ASN
GLY
ASP
LEU
LYS
TYR
• Molecule 1: Sodium-dependent neutral amino acid transporter B(0)AT1
Chain C:
MET
ALA
ASP
TYR
LYS
ASP
ASP
ASP
ASP
LYS
SER
GLY
PRO
ASP
GLU
VAL
ASP
ALA
SER
GLY
ARG
VAL
ARG
LEU
V5 L6 P7 N8 R14
S17
L18
A19
E20
L21
E22
T23
I24
E25
Q26
E27
E28
R32
K38
G51
L52
G53
W56
R57
L75
I76
L77
L78
V79
L80
E81
G82
I83
P84
L85
R97
S105
L111
K112
G113
L114
L120
Y129
L181
N182
I183
W205
S206
I213
T219
V223
Y224
I225
T226
L229
P230
Y231
V232
V233
L234
T235
I236
F237
L238
E261
L262
A263
Q264
W268
Q274
S278
F289
S290
S291
V295
H296
N297
S307
V317
Q331
R332
Y333
D334
D335
C336
F337
I341
L350
P351
N354
V355
T356
Q357
E358
V361
Q364
C383
F388
V393
L398
V402
K409
L427
S430
M436
E437
G438
V439
V440
V441
P442
L443
L461
I462
C463
L464
G465
T466
I497
M502
V508
V511
F520
H524
W530
T533
W534
R535
V536
V537
K572
S573
Y578
V582
Y583
V584
V587
I588
V589
A590
G591
V592
P593
S594
L595
T596
I597
P598
G599
Y600
K604
L605
H609
CYS
GLN
LYS
PRO
GLY
ASP
HIS
GLN
GLY
LEU
VAL
SER
THR
LEU
SER
THR
ALA
SER
MET
ASN
GLY
ASP
LEU
LYS
TYR
• Molecule 2: Angiotensin-converting enzyme 2
Page 10 Full wwPDB EM Model Validation Report 6M18
Chain B:ME
TAR
GSE
RSE
RSE
RSE
RTR
PLE
ULE
ULE
USE
RLE
UVA
LAL
AVA
LTH
RAL
AAL
ATR
PSE
RHI
SPR
OGL
NPH
EGL
ULY
SGL
NSE
RT2
0I2
1
L45
A46
S47
W48
N49
Y50
N51
T52
N53
I54
T55
E56
V59
Q60
N63
P84
L85
N90
V93
Q98
N103
S109
K112
K131
V132
C133
Y183
N194
Y243
K247
W302
I307
K341
A342
V343
C344
L359
D367
K476
D509
S611
A614
K619
I622
R644
E667
R678
I679
S680
P696
E699
S709
R716
L725
P738
V739
V749
M750
G751
V752
I753
V754
V755
G756
I757
V758
I759
L760
I761
R768
LYS
LYS
LYS
ASN
LYS
ALA
ARG
SER
GLY
GLU
ASN
PRO
TYR
ALA
SER
ILE
ASP
ILE
SER
LYS
GLY
GLU
ASN
ASN
PRO
GLY
PHE
GLN
ASN
THR
ASP
ASP
VAL
GLN
THR
SER
PHE
• Molecule 2: Angiotensin-converting enzyme 2
Chain D:
MET
ARG
SER
SER
SER
SER
TRP
LEU
LEU
LEU
SER
LEU
VAL
ALA
VAL
THR
ALA
ALA
TRP
SER
HIS
PRO
GLN
PHE
GLU
LYS
GLN
SER
T20
I21
L45
A46
S47
W48
N49
Y50
N51
T52
N53
I54
T55
E56
V59
Q60
N61
M62
N63
G66
P84
L85
N90
V93
Q98
N103
S109
K112
C133
D136
Y183
N194
Y243
K247
W302
I307
K341
A342
V343
C344
L359
D367
D509
I513
S611
A614
K619
I622
R644
E667
P677
R678
I679
S680
P696
E699
S709
R716
L725
P738
V739
V749
M750
G751
V752
I753
V754
V755
G756
I757
V758
I759
L760
I761
R768
LYS
LYS
LYS
ASN
LYS
ALA
ARG
SER
GLY
GLU
ASN
PRO
TYR
ALA
SER
ILE
ASP
ILE
SER
LYS
GLY
GLU
ASN
ASN
PRO
GLY
PHE
GLN
ASN
THR
ASP
ASP
VAL
GLN
THR
SER
PHE
Page 11 Full wwPDB EM Model Validation Report 6M18
4 Experimental information i○
Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C2 DepositorNumber of particles used 418140 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 K3 BIOQUANTUM (6k x 4k) Depositor
Page 12 Full wwPDB EM Model Validation Report 6M18
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: 3PH,ZN, NAG
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 0.47 0/4934 0.63 0/67401 C 0.47 0/4934 0.63 0/67402 B 0.34 0/6258 0.51 0/84962 D 0.34 0/6258 0.51 0/8496All All 0.41 0/22384 0.57 0/30472
There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.
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 4794 0 4748 145 01 C 4794 0 4748 145 02 B 6095 0 5907 44 02 D 6095 0 5907 46 03 A 84 0 76 0 03 B 182 0 163 0 03 C 84 0 76 0 03 D 182 0 163 0 04 A 96 0 150 1 0
Continued on next page...
Page 13 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes4 C 96 0 150 0 05 B 1 0 0 0 05 D 1 0 0 0 06 A 10 0 0 0 06 B 5 0 0 0 06 C 10 0 0 0 06 D 5 0 0 0 0All All 22534 0 22088 377 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 (377) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:85:LEU:HD22 1:A:502:MET:CE 1.70 1.211:C:85:LEU:HD22 1:C:502:MET:CE 1.70 1.201:C:592:VAL:O 1:C:596:THR:HG23 1.44 1.151:A:584:VAL:O 1:A:588:ILE:HG23 1.43 1.151:A:592:VAL:O 1:A:596:THR:HG23 1.44 1.151:C:584:VAL:O 1:C:588:ILE:HG23 1.43 1.15
1:A:331:GLN:HG2 1:A:409:LYS:HE3 1.33 1.111:A:85:LEU:HD22 1:A:502:MET:HE3 1.30 1.091:C:331:GLN:HG2 1:C:409:LYS:HE3 1.33 1.051:C:85:LEU:HD22 1:C:502:MET:HE1 1.37 1.021:A:331:GLN:HG2 1:A:409:LYS:CE 1.90 1.011:C:331:GLN:HG2 1:C:409:LYS:CE 1.90 0.991:C:85:LEU:HD22 1:C:502:MET:HE3 1.42 0.981:C:583:TYR:O 1:C:587:VAL:HG23 1.66 0.961:A:583:TYR:O 1:A:587:VAL:HG23 1.66 0.94
1:A:85:LEU:HD22 1:A:502:MET:HE1 1.48 0.931:A:226:THR:O 1:A:230:PRO:HD3 1.72 0.901:A:226:THR:O 1:A:230:PRO:CD 2.20 0.901:C:226:THR:O 1:C:230:PRO:HD3 1.72 0.901:C:226:THR:O 1:C:230:PRO:CD 2.20 0.89
1:A:21:LEU:HD22 1:A:24:ILE:HG21 1.54 0.891:C:85:LEU:CD2 1:C:502:MET:CE 2.51 0.891:C:21:LEU:HD22 1:C:24:ILE:HG21 1.54 0.881:A:85:LEU:CD2 1:A:502:MET:HE3 2.04 0.881:A:85:LEU:CD2 1:A:502:MET:CE 2.51 0.871:A:597:ILE:HB 1:A:598:PRO:HD3 1.56 0.87
Continued on next page...
Page 14 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:79:VAL:O 1:A:80:LEU:HD23 1.75 0.871:C:79:VAL:O 1:C:80:LEU:HD23 1.75 0.861:C:597:ILE:HB 1:C:598:PRO:HD3 1.56 0.861:A:17:SER:HB3 1:A:20:GLU:HG2 1.58 0.861:C:219:THR:O 1:C:223:VAL:HG13 1.78 0.831:A:331:GLN:CG 1:A:409:LYS:HE3 2.08 0.831:C:17:SER:HB3 1:C:20:GLU:HG2 1.58 0.831:A:219:THR:O 1:A:223:VAL:HG13 1.78 0.83
1:A:226:THR:HG21 1:A:430:SER:HB3 1.61 0.831:A:21:LEU:CD2 1:A:24:ILE:HG21 2.09 0.821:A:592:VAL:O 1:A:596:THR:CG2 2.28 0.821:C:331:GLN:CG 1:C:409:LYS:HE3 2.08 0.82
1:C:226:THR:HG21 1:C:430:SER:HB3 1.61 0.811:C:21:LEU:CD2 1:C:24:ILE:HG21 2.09 0.811:C:85:LEU:CD2 1:C:502:MET:HE1 2.12 0.791:A:589:VAL:O 1:A:593:PRO:HD2 1.82 0.791:C:589:VAL:O 1:C:593:PRO:HD2 1.82 0.791:C:583:TYR:O 1:C:587:VAL:CG2 2.30 0.791:C:592:VAL:O 1:C:596:THR:CG2 2.28 0.791:A:583:TYR:O 1:A:587:VAL:CG2 2.30 0.782:D:757:ILE:O 2:D:761:ILE:HG23 1.85 0.762:B:757:ILE:O 2:B:761:ILE:HG23 1.85 0.76
1:A:213:ILE:HG21 2:B:760:LEU:HD13 1.69 0.751:C:213:ILE:HG21 2:D:760:LEU:HD13 1.69 0.751:C:436:MET:O 1:C:436:MET:HG3 1.87 0.741:C:597:ILE:HB 1:C:598:PRO:CD 2.18 0.731:C:226:THR:O 1:C:230:PRO:HD2 1.88 0.721:A:597:ILE:HB 1:A:598:PRO:CD 2.18 0.72
1:A:589:VAL:HG23 1:A:590:ALA:N 2.04 0.721:C:589:VAL:HG23 1:C:590:ALA:N 2.04 0.721:C:85:LEU:CD2 1:C:502:MET:HE3 2.16 0.721:A:226:THR:O 1:A:230:PRO:HD2 1.88 0.722:D:622:ILE:HB 2:D:679:ILE:CG2 2.19 0.722:B:622:ILE:HB 2:B:679:ILE:CG2 2.19 0.721:A:436:MET:O 1:A:436:MET:HG3 1.87 0.72
1:A:332:ARG:HH21 1:A:388:PHE:HE1 1.37 0.711:A:230:PRO:O 1:A:234:LEU:HB2 1.92 0.701:C:262:LEU:O 1:C:264:GLN:N 2.23 0.701:C:230:PRO:O 1:C:234:LEU:HB2 1.92 0.70
1:A:21:LEU:HD22 1:A:24:ILE:CG2 2.22 0.691:C:21:LEU:O 1:C:23:THR:N 2.26 0.69
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Page 15 Full wwPDB EM Model Validation Report 6M18
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:21:LEU:O 1:A:23:THR:N 2.26 0.691:A:589:VAL:HG23 1:A:590:ALA:H 1.57 0.691:A:332:ARG:NH2 1:A:388:PHE:CE1 2.60 0.691:C:21:LEU:C 1:C:23:THR:H 1.96 0.69
1:C:332:ARG:NH2 1:C:388:PHE:CE1 2.60 0.691:C:21:LEU:HD22 1:C:24:ILE:CG2 2.22 0.681:C:589:VAL:HG23 1:C:590:ALA:H 1.57 0.681:C:332:ARG:HH21 1:C:388:PHE:HE1 1.37 0.68
1:A:21:LEU:C 1:A:23:THR:H 1.96 0.681:A:350:LEU:O 1:A:351:PRO:O 2.12 0.68
1:A:356:THR:OG1 1:A:357:GLN:N 2.27 0.671:A:588:ILE:HD12 1:A:589:VAL:N 2.10 0.671:A:83:ILE:CD1 1:A:307:SER:CB 2.73 0.671:C:350:LEU:O 1:C:351:PRO:O 2.12 0.66
1:C:205:TRP:CZ2 1:C:466:THR:CG2 2.79 0.661:C:588:ILE:HD12 1:C:589:VAL:N 2.10 0.661:A:205:TRP:CZ2 1:A:466:THR:CG2 2.79 0.651:A:85:LEU:CD2 1:A:502:MET:HE1 2.24 0.651:C:83:ILE:CD1 1:C:307:SER:CB 2.73 0.65
1:A:332:ARG:NH2 1:A:388:PHE:CD1 2.65 0.651:C:38:LYS:HE3 1:C:297:ASN:HD21 1.62 0.65
1:C:592:VAL:HG12 1:C:593:PRO:HD3 1.79 0.651:A:588:ILE:HG13 1:A:589:VAL:H 1.62 0.641:A:262:LEU:O 1:A:264:GLN:N 2.23 0.641:A:38:LYS:HE3 1:A:297:ASN:HD21 1.62 0.64
1:A:592:VAL:HG12 1:A:593:PRO:HD3 1.79 0.641:C:332:ARG:NH2 1:C:388:PHE:CD1 2.65 0.641:C:588:ILE:HG13 1:C:589:VAL:H 1.62 0.641:A:21:LEU:O 1:A:24:ILE:HG22 1.98 0.631:C:21:LEU:O 1:C:24:ILE:HG22 1.98 0.632:D:622:ILE:HB 2:D:679:ILE:HG21 1.80 0.632:D:752:VAL:O 2:D:755:VAL:HG12 1.99 0.63
1:C:356:THR:OG1 1:C:357:GLN:N 2.27 0.622:B:752:VAL:O 2:B:755:VAL:HG12 1.99 0.622:D:751:GLY:O 2:D:754:VAL:HG22 1.99 0.622:B:622:ILE:HB 2:B:679:ILE:HG21 1.80 0.612:B:751:GLY:O 2:B:754:VAL:HG22 1.99 0.611:C:83:ILE:HD11 1:C:307:SER:OG 2.01 0.611:A:53:GLY:O 1:A:57:ARG:HB3 2.01 0.60
2:D:619:LYS:HD3 2:D:725:LEU:HD22 1.83 0.601:A:331:GLN:HA 1:A:331:GLN:OE1 2.02 0.60
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Page 16 Full wwPDB EM Model Validation Report 6M18
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:53:GLY:O 1:C:57:ARG:HB3 2.01 0.601:C:595:LEU:O 1:C:598:PRO:HD2 2.01 0.601:C:83:ILE:CD1 1:C:307:SER:OG 2.50 0.60
1:A:443:LEU:HD23 1:A:462:ILE:HD11 1.84 0.601:A:595:LEU:O 1:A:598:PRO:HD2 2.01 0.601:C:6:LEU:HB3 1:C:7:PRO:HD2 1.85 0.591:A:83:ILE:CD1 1:A:307:SER:OG 2.50 0.591:A:83:ILE:HD11 1:A:307:SER:OG 2.01 0.591:A:511:VAL:HG11 1:A:535:ARG:HE 1.67 0.592:D:622:ILE:HB 2:D:679:ILE:HG22 1.85 0.591:A:6:LEU:HB3 1:A:7:PRO:HD2 1.85 0.591:C:6:LEU:HB3 1:C:7:PRO:CD 2.32 0.592:B:619:LYS:HD3 2:B:725:LEU:HD22 1.83 0.591:A:24:ILE:O 1:A:27:GLU:HG3 2.03 0.58
1:C:331:GLN:OE1 1:C:331:GLN:HA 2.02 0.581:C:443:LEU:HD23 1:C:462:ILE:HD11 1.84 0.581:A:355:VAL:O 1:A:355:VAL:HG12 2.03 0.581:A:6:LEU:HB3 1:A:7:PRO:CD 2.32 0.581:A:28:GLU:OE2 1:A:97:ARG:NH1 2.36 0.581:C:355:VAL:O 1:C:355:VAL:HG12 2.03 0.58
1:C:356:THR:HG23 1:C:358:GLU:HG3 1.85 0.581:C:24:ILE:O 1:C:27:GLU:HG3 2.03 0.58
1:C:56:TRP:HA 1:C:398:LEU:HD23 1.86 0.581:C:28:GLU:OE2 1:C:97:ARG:NH1 2.36 0.581:C:21:LEU:C 1:C:23:THR:N 2.58 0.57
1:C:511:VAL:HG11 1:C:535:ARG:HE 1.67 0.572:D:749:VAL:O 2:D:752:VAL:HG22 2.04 0.57
1:C:205:TRP:CZ2 1:C:466:THR:HG21 2.40 0.572:B:622:ILE:HB 2:B:679:ILE:HG22 1.85 0.57
1:A:356:THR:HG23 1:A:358:GLU:HG3 1.85 0.571:A:226:THR:CG2 1:A:430:SER:HB3 2.33 0.571:C:226:THR:CG2 1:C:430:SER:HB3 2.33 0.572:D:611:SER:HB3 2:D:614:ALA:HB2 1.86 0.571:A:21:LEU:C 1:A:23:THR:N 2.58 0.57
1:C:51:GLY:HA2 1:C:427:LEU:HG 1.87 0.571:A:51:GLY:HA2 1:A:427:LEU:HG 1.87 0.572:B:749:VAL:O 2:B:752:VAL:HG22 2.04 0.56
2:D:644:ARG:NH1 2:D:667:GLU:OE1 2.38 0.562:D:341:LYS:O 2:D:342:ALA:HB2 2.05 0.561:A:56:TRP:HA 1:A:398:LEU:HD23 1.86 0.562:B:85:LEU:HD21 2:B:98:GLN:HG2 1.86 0.56
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Page 17 Full wwPDB EM Model Validation Report 6M18
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
2:D:85:LEU:HD21 2:D:98:GLN:HG2 1.86 0.562:B:678:ARG:O 2:B:679:ILE:HB 2.06 0.562:B:611:SER:HB3 2:B:614:ALA:HB2 1.86 0.561:A:205:TRP:CZ2 1:A:466:THR:HG21 2.40 0.562:B:644:ARG:NH1 2:B:667:GLU:OE1 2.38 0.561:A:17:SER:CB 1:A:20:GLU:HG2 2.33 0.551:C:25:GLU:HA 1:C:28:GLU:HG2 1.88 0.552:B:341:LYS:O 2:B:342:ALA:HB2 2.05 0.552:D:678:ARG:O 2:D:679:ILE:HB 2.06 0.55
1:C:393:VAL:HG11 1:C:402:VAL:HG21 1.89 0.551:A:393:VAL:HG11 1:A:402:VAL:HG21 1.89 0.541:A:25:GLU:HA 1:A:28:GLU:HG2 1.88 0.541:C:18:LEU:CD1 1:C:520:PHE:CD2 2.91 0.541:A:18:LEU:CD1 1:A:520:PHE:CD2 2.91 0.541:C:21:LEU:CD2 1:C:24:ILE:CG2 2.83 0.541:C:274:GLN:O 1:C:278:SER:N 2.38 0.541:C:17:SER:CB 1:C:20:GLU:HG2 2.33 0.541:A:597:ILE:CB 1:A:598:PRO:HD3 2.35 0.532:D:103:ASN:HB2 2:D:194:ASN:HD21 1.73 0.531:A:181:LEU:O 1:A:182:ASN:HB3 2.08 0.53
1:C:592:VAL:HG12 1:C:593:PRO:CD 2.38 0.531:A:592:VAL:HG12 1:A:593:PRO:CD 2.38 0.531:A:83:ILE:HB 1:A:84:PRO:HD3 1.91 0.53
2:B:103:ASN:HB2 2:B:194:ASN:HD21 1.73 0.531:C:588:ILE:CG1 1:C:589:VAL:N 2.72 0.531:C:77:LEU:O 1:C:81:GLU:HG2 2.09 0.531:A:8:ASN:ND2 1:A:508:VAL:O 2.42 0.531:C:8:ASN:ND2 1:C:508:VAL:O 2.42 0.531:A:572:LYS:HG3 1:A:573:SER:H 1.74 0.531:A:77:LEU:O 1:A:81:GLU:HG2 2.09 0.531:C:83:ILE:HB 1:C:84:PRO:HD3 1.91 0.531:C:181:LEU:O 1:C:182:ASN:HB3 2.08 0.521:C:588:ILE:CD1 1:C:589:VAL:N 2.73 0.521:C:589:VAL:CG2 1:C:590:ALA:N 2.73 0.521:A:592:VAL:HB 1:A:593:PRO:HD2 1.92 0.521:A:274:GLN:O 1:A:278:SER:N 2.38 0.521:A:588:ILE:CG1 1:A:589:VAL:N 2.72 0.521:C:18:LEU:HD12 1:C:520:PHE:CD2 2.44 0.521:A:18:LEU:HD12 1:A:520:PHE:CD2 2.44 0.521:C:592:VAL:HB 1:C:593:PRO:HD2 1.92 0.522:D:47:SER:O 2:D:51:ASN:ND2 2.41 0.52
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Page 18 Full wwPDB EM Model Validation Report 6M18
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:337:PHE:CD2 1:A:357:GLN:OE1 2.63 0.521:C:337:PHE:CD2 1:C:357:GLN:OE1 2.63 0.521:C:524:HIS:ND1 1:C:524:HIS:O 2.43 0.511:A:588:ILE:CD1 1:A:589:VAL:N 2.73 0.511:C:572:LYS:HG3 1:C:573:SER:H 1.74 0.511:A:112:LYS:HD3 1:A:600:TYR:CZ 2.46 0.512:B:47:SER:O 2:B:51:ASN:ND2 2.41 0.51
1:C:112:LYS:HD3 1:C:600:TYR:CZ 2.46 0.511:A:589:VAL:CG2 1:A:590:ALA:N 2.73 0.511:A:588:ILE:O 1:A:592:VAL:HG23 2.11 0.51
1:A:524:HIS:ND1 1:A:524:HIS:O 2.43 0.511:A:589:VAL:CG2 1:A:590:ALA:H 2.24 0.501:C:588:ILE:O 1:C:592:VAL:HG23 2.11 0.501:C:6:LEU:CB 1:C:7:PRO:CD 2.88 0.502:D:45:LEU:O 2:D:49:ASN:ND2 2.44 0.50
1:A:21:LEU:CD2 1:A:24:ILE:CG2 2.83 0.501:A:592:VAL:HB 1:A:593:PRO:CD 2.42 0.501:C:592:VAL:HB 1:C:593:PRO:CD 2.42 0.502:B:45:LEU:O 2:B:49:ASN:ND2 2.44 0.501:C:597:ILE:CB 1:C:598:PRO:CD 2.89 0.502:D:20:THR:O 2:D:20:THR:OG1 2.29 0.501:A:6:LEU:CB 1:A:7:PRO:CD 2.88 0.49
2:D:759:ILE:HG22 2:D:759:ILE:O 2.12 0.491:A:205:TRP:CZ2 1:A:466:THR:HG22 2.46 0.491:C:439:VAL:O 1:C:439:VAL:HG12 2.12 0.49
1:C:205:TRP:CZ2 1:C:466:THR:HG22 2.46 0.491:C:597:ILE:CB 1:C:598:PRO:HD3 2.35 0.49
1:A:439:VAL:HG12 1:A:439:VAL:O 2.12 0.482:B:759:ILE:O 2:B:759:ILE:HG22 2.12 0.48
1:C:437:GLU:HA 1:C:437:GLU:OE1 2.14 0.481:C:105:SER:HB2 1:C:112:LYS:HG3 1.95 0.481:C:26:GLN:N 1:C:26:GLN:OE1 2.47 0.48
2:D:302:TRP:HE3 2:D:307:ILE:HG22 1.78 0.481:A:597:ILE:CB 1:A:598:PRO:CD 2.89 0.481:A:105:SER:HB2 1:A:112:LYS:HG3 1.95 0.482:B:302:TRP:HE3 2:B:307:ILE:HG22 1.78 0.482:B:52:THR:O 2:B:342:ALA:HB2 2.14 0.481:A:26:GLN:N 1:A:26:GLN:OE1 2.47 0.48
1:A:588:ILE:HG13 1:A:589:VAL:N 2.28 0.481:C:21:LEU:HA 1:C:21:LEU:HD23 1.79 0.482:D:52:THR:O 2:D:342:ALA:HB2 2.14 0.48
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Page 19 Full wwPDB EM Model Validation Report 6M18
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:437:GLU:OE1 1:A:437:GLU:HA 2.14 0.471:C:233:VAL:O 1:C:233:VAL:HG12 2.15 0.471:C:588:ILE:CG1 1:C:589:VAL:H 2.27 0.471:A:331:GLN:CG 1:A:409:LYS:CE 2.77 0.471:A:331:GLN:HG2 1:A:409:LYS:NZ 2.30 0.472:B:54:ILE:HG12 2:B:342:ALA:HA 1.97 0.471:C:588:ILE:HG13 1:C:589:VAL:N 2.28 0.471:C:589:VAL:CG2 1:C:590:ALA:H 2.24 0.471:C:79:VAL:HG23 1:C:79:VAL:O 2.14 0.472:B:20:THR:OG1 2:B:20:THR:O 2.29 0.471:A:111:LEU:O 1:A:113:GLY:N 2.40 0.461:A:354:ASN:N 1:A:354:ASN:OD1 2.41 0.461:A:79:VAL:O 1:A:79:VAL:HG23 2.14 0.461:C:583:TYR:O 1:C:587:VAL:CB 2.64 0.46
1:A:233:VAL:HG12 1:A:233:VAL:O 2.15 0.462:B:679:ILE:O 2:B:679:ILE:HG22 2.15 0.46
1:C:25:GLU:HG3 1:C:295:VAL:HG23 1.97 0.461:C:331:GLN:HG2 1:C:409:LYS:NZ 2.30 0.462:D:754:VAL:HG23 2:D:755:VAL:N 2.31 0.461:A:83:ILE:HG22 1:A:530:TRP:CH2 2.51 0.462:D:679:ILE:O 2:D:679:ILE:HG22 2.15 0.46
1:A:25:GLU:HG3 1:A:295:VAL:HG23 1.97 0.462:D:54:ILE:HG12 2:D:342:ALA:HA 1.97 0.461:A:583:TYR:O 1:A:587:VAL:CB 2.64 0.462:B:709:SER:OG 2:D:716:ARG:NH1 2.49 0.462:B:678:ARG:HG3 2:B:678:ARG:O 2.16 0.461:C:111:LEU:O 1:C:113:GLY:N 2.40 0.462:D:183:TYR:OH 2:D:509:ASP:OD1 2.32 0.461:C:341:ILE:HG23 1:C:355:VAL:HG12 1.99 0.451:C:83:ILE:HG22 1:C:530:TRP:CH2 2.51 0.451:C:229:LEU:O 1:C:231:TYR:N 2.50 0.452:B:60:GLN:HA 2:B:63:ASN:HB2 1.98 0.451:A:229:LEU:HB3 1:A:230:PRO:HD3 1.99 0.451:A:25:GLU:C 1:A:27:GLU:H 2.20 0.45
1:A:56:TRP:CD1 1:A:56:TRP:C 2.90 0.452:B:754:VAL:HG23 2:B:755:VAL:N 2.31 0.45
1:C:25:GLU:C 1:C:27:GLU:H 2.20 0.452:B:716:ARG:NH1 2:D:709:SER:OG 2.49 0.451:A:56:TRP:O 1:A:56:TRP:CD1 2.70 0.44
2:B:183:TYR:OH 2:B:509:ASP:OD1 2.32 0.442:D:678:ARG:O 2:D:678:ARG:HG3 2.16 0.44
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Page 20 Full wwPDB EM Model Validation Report 6M18
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:56:TRP:CD1 1:C:56:TRP:C 2.90 0.442:D:60:GLN:HA 2:D:63:ASN:HB2 1.98 0.44
1:A:341:ILE:HG23 1:A:355:VAL:HG12 1.99 0.441:C:32:ARG:NH2 1:C:291:SER:O 2.51 0.441:A:32:ARG:NH2 1:A:291:SER:O 2.51 0.442:D:752:VAL:HG23 2:D:753:ILE:N 2.31 0.441:A:229:LEU:O 1:A:231:TYR:N 2.50 0.441:C:238:LEU:O 1:C:238:LEU:HD12 2.18 0.44
1:C:354:ASN:OD1 1:C:354:ASN:N 2.41 0.441:C:83:ILE:HD11 1:C:307:SER:CB 2.46 0.441:A:18:LEU:HD11 1:A:520:PHE:CD2 2.52 0.441:C:229:LEU:HB3 1:C:230:PRO:HD3 1.99 0.442:D:109:SER:HB3 2:D:112:LYS:HB2 2.00 0.441:C:56:TRP:CD1 1:C:56:TRP:O 2.70 0.441:A:17:SER:HB3 1:A:20:GLU:CG 2.40 0.441:A:262:LEU:C 1:A:264:GLN:H 2.16 0.44
2:B:752:VAL:HG23 2:B:753:ILE:N 2.31 0.441:A:441:VAL:HB 1:A:442:PRO:HD3 2.00 0.43
1:C:234:LEU:HD11 1:C:317:VAL:HG22 2.00 0.432:B:109:SER:HB3 2:B:112:LYS:HB2 2.00 0.431:C:262:LEU:C 1:C:264:GLN:H 2.16 0.43
2:D:696:PRO:HG2 2:D:699:GLU:HG3 2.00 0.431:A:238:LEU:HD12 1:A:238:LEU:O 2.18 0.432:D:760:LEU:HA 2:D:760:LEU:HD23 1.77 0.432:B:696:PRO:HG2 2:B:699:GLU:HG3 2.00 0.432:D:136:ASP:OD1 2:D:136:ASP:N 2.47 0.432:B:56:GLU:HA 2:B:59:VAL:HG23 2.01 0.431:C:441:VAL:HB 1:C:442:PRO:HD3 2.00 0.431:C:18:LEU:HD11 1:C:520:PHE:CD2 2.52 0.431:A:443:LEU:HA 1:A:443:LEU:HD12 1.86 0.432:D:56:GLU:HA 2:D:59:VAL:HG23 2.01 0.43
2:B:760:LEU:HD23 2:B:760:LEU:HA 1.77 0.431:C:443:LEU:HA 1:C:443:LEU:HD12 1.86 0.431:C:56:TRP:O 1:C:56:TRP:HD1 2.02 0.43
2:D:367:ASP:OD1 2:D:367:ASP:N 2.52 0.431:A:234:LEU:HD11 1:A:317:VAL:HG22 2.00 0.421:C:337:PHE:HD2 1:C:357:GLN:CD 2.22 0.421:C:229:LEU:C 1:C:231:TYR:N 2.73 0.421:A:235:THR:O 1:A:238:LEU:N 2.42 0.421:A:334:ASP:C 1:A:336:CYS:H 2.23 0.42
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Page 21 Full wwPDB EM Model Validation Report 6M18
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:592:VAL:CG1 1:C:593:PRO:HD3 2.47 0.421:A:337:PHE:HD2 1:A:357:GLN:CD 2.22 0.421:C:592:VAL:CB 1:C:593:PRO:CD 2.97 0.421:C:17:SER:HB3 1:C:20:GLU:CG 2.40 0.421:A:595:LEU:O 1:A:597:ILE:N 2.53 0.422:B:90:ASN:HB3 2:B:93:VAL:HG12 2.02 0.421:C:334:ASP:C 1:C:336:CYS:H 2.23 0.421:A:264:GLN:O 1:A:268:TRP:HD1 2.03 0.421:A:592:VAL:CB 1:A:593:PRO:CD 2.97 0.422:B:343:VAL:O 2:B:359:LEU:HD21 2.20 0.421:C:235:THR:C 1:C:237:PHE:N 2.73 0.42
1:C:114:LEU:HD23 1:C:497:ILE:HG23 2.02 0.422:D:343:VAL:O 2:D:359:LEU:HD21 2.20 0.421:A:262:LEU:C 1:A:264:GLN:N 2.73 0.42
1:A:592:VAL:CG1 1:A:593:PRO:HD3 2.47 0.421:A:235:THR:C 1:A:237:PHE:N 2.73 0.41
2:D:738:PRO:HG2 2:D:739:VAL:HG23 2.02 0.411:A:229:LEU:C 1:A:231:TYR:N 2.73 0.412:B:51:ASN:O 2:B:342:ALA:HB1 2.20 0.412:D:62:MET:O 2:D:66:GLY:N 2.49 0.41
1:A:443:LEU:CD2 1:A:462:ILE:HD11 2.50 0.414:A:708:3PH:H3E2 4:A:708:3PH:H3H1 1.88 0.412:B:21:ILE:HD11 2:B:84:PRO:HD2 2.03 0.412:B:476:LYS:HA 2:B:476:LYS:HD3 1.89 0.411:C:289:PHE:CE1 1:C:437:GLU:HG2 2.56 0.411:A:83:ILE:HG22 1:A:530:TRP:HH2 1.85 0.412:B:738:PRO:HG2 2:B:739:VAL:HG23 2.02 0.411:C:264:GLN:O 1:C:268:TRP:HD1 2.03 0.41
2:B:752:VAL:CG2 2:B:753:ILE:N 2.84 0.412:D:90:ASN:HB3 2:D:93:VAL:HG12 2.02 0.411:A:83:ILE:CG2 1:A:530:TRP:HH2 2.33 0.412:B:243:TYR:OH 2:B:247:LYS:NZ 2.53 0.411:A:336:CYS:SG 1:A:383:CYS:CB 3.07 0.411:C:83:ILE:HG22 1:C:530:TRP:HH2 1.85 0.411:A:25:GLU:HG3 1:A:295:VAL:CG2 2.51 0.411:C:350:LEU:C 1:C:351:PRO:O 2.59 0.412:D:51:ASN:O 2:D:342:ALA:HB1 2.20 0.411:A:18:LEU:HA 1:A:18:LEU:HD13 1.94 0.412:D:677:PRO:C 2:D:679:ILE:N 2.73 0.411:A:361:VAL:HA 1:A:364:GLN:HB2 2.03 0.411:A:18:LEU:HD12 1:A:520:PHE:CE2 2.56 0.41
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Page 22 Full wwPDB EM Model Validation Report 6M18
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:C:578:TYR:HB3 1:C:582:VAL:HG11 2.03 0.411:C:595:LEU:O 1:C:597:ILE:N 2.53 0.411:A:350:LEU:C 1:A:351:PRO:O 2.59 0.402:B:131:LYS:HE2 2:B:131:LYS:HB3 1.82 0.401:C:229:LEU:C 1:C:231:TYR:H 2.24 0.401:C:336:CYS:SG 1:C:383:CYS:CB 3.07 0.401:C:18:LEU:HD12 1:C:520:PHE:CE2 2.56 0.401:A:56:TRP:O 1:A:56:TRP:HD1 2.02 0.402:B:367:ASP:N 2:B:367:ASP:OD1 2.52 0.401:C:361:VAL:HA 1:C:364:GLN:HB2 2.03 0.402:D:513:ILE:HD12 2:D:513:ILE:HA 1.95 0.401:A:289:PHE:CE1 1:A:437:GLU:HG2 2.56 0.401:A:586:VAL:O 1:A:589:VAL:HG22 2.22 0.401:C:262:LEU:C 1:C:264:GLN:N 2.73 0.401:C:533:THR:HA 1:C:537:VAL:HB 2.04 0.402:D:21:ILE:HD11 2:D:84:PRO:HD2 2.03 0.402:D:243:TYR:OH 2:D:247:LYS:NZ 2.53 0.401:C:235:THR:O 1:C:238:LEU:N 2.42 0.401:C:25:GLU:HG3 1:C:295:VAL:CG2 2.51 0.401:C:83:ILE:CG2 1:C:530:TRP:HH2 2.33 0.401:A:354:ASN:O 1:A:355:VAL:HB 2.22 0.401:A:6:LEU:HA 1:A:6:LEU:HD23 1.89 0.40
2:D:752:VAL:CG2 2:D:753:ILE:N 2.84 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 603/654 (92%) 506 (84%) 79 (13%) 18 (3%) 5 19
1 C 603/654 (92%) 506 (84%) 79 (13%) 18 (3%) 5 19Continued on next page...
Page 23 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Mol Chain Analysed Favoured Allowed Outliers Percentiles
2 B 747/814 (92%) 716 (96%) 29 (4%) 2 (0%) 43 75
2 D 747/814 (92%) 716 (96%) 29 (4%) 2 (0%) 43 75
All All 2700/2936 (92%) 2444 (90%) 216 (8%) 40 (2%) 16 37
All (40) Ramachandran outliers are listed below:
Mol Chain Res Type1 A 6 LEU1 A 7 PRO1 A 112 LYS1 A 183 ILE1 A 263 ALA1 A 351 PRO1 A 592 VAL1 A 596 THR1 C 6 LEU1 C 7 PRO1 C 112 LYS1 C 183 ILE1 C 263 ALA1 C 351 PRO1 C 592 VAL1 C 596 THR1 A 22 GLU1 A 226 THR1 A 588 ILE2 B 679 ILE1 C 22 GLU1 C 226 THR1 C 588 ILE2 D 679 ILE1 A 18 LEU1 C 18 LEU1 A 79 VAL1 C 79 VAL1 A 224 TYR1 A 354 ASN2 B 342 ALA1 C 224 TYR1 C 354 ASN2 D 342 ALA
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Page 24 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Mol Chain Res Type1 A 597 ILE1 C 597 ILE1 A 225 ILE1 C 225 ILE1 A 355 VAL1 C 355 VAL
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 527/572 (92%) 499 (95%) 28 (5%) 25 58
1 C 527/572 (92%) 499 (95%) 28 (5%) 25 58
2 B 662/720 (92%) 658 (99%) 4 (1%) 87 96
2 D 662/720 (92%) 658 (99%) 4 (1%) 87 96
All All 2378/2584 (92%) 2314 (97%) 64 (3%) 51 80
All (64) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type1 A 8 ASN1 A 14 ARG1 A 18 LEU1 A 20 GLU1 A 26 GLN1 A 57 ARG1 A 75 LEU1 A 78 LEU1 A 80 LEU1 A 85 LEU1 A 114 LEU1 A 120 LEU1 A 129 TYR1 A 206 SER1 A 229 LEU
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Page 25 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Mol Chain Res Type1 A 234 LEU1 A 237 PHE1 A 261 GLU1 A 354 ASN1 A 356 THR1 A 436 MET1 A 443 LEU1 A 461 LEU1 A 464 LEU1 A 588 ILE1 A 595 LEU1 A 604 LYS1 A 605 LEU2 B 133 CYS2 B 344 CYS2 B 680 SER2 B 761 ILE1 C 8 ASN1 C 14 ARG1 C 18 LEU1 C 20 GLU1 C 26 GLN1 C 57 ARG1 C 75 LEU1 C 78 LEU1 C 80 LEU1 C 85 LEU1 C 114 LEU1 C 120 LEU1 C 129 TYR1 C 206 SER1 C 229 LEU1 C 234 LEU1 C 237 PHE1 C 261 GLU1 C 354 ASN1 C 356 THR1 C 436 MET1 C 443 LEU1 C 461 LEU1 C 464 LEU1 C 588 ILE
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Continued from previous page...Mol Chain Res Type1 C 595 LEU1 C 604 LYS1 C 605 LEU2 D 133 CYS2 D 344 CYS2 D 680 SER2 D 761 ILE
Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (29) suchsidechains are listed below:
Mol Chain Res Type1 A 159 GLN1 A 293 ASN1 A 297 ASN2 B 33 ASN2 B 42 GLN2 B 64 ASN2 B 98 GLN2 B 101 GLN2 B 194 ASN2 B 373 HIS2 B 505 HIS2 B 586 ASN2 B 599 ASN2 B 718 ASN1 C 159 GLN1 C 293 ASN1 C 297 ASN2 D 33 ASN2 D 42 GLN2 D 64 ASN2 D 98 GLN2 D 101 GLN2 D 117 ASN2 D 194 ASN2 D 373 HIS2 D 505 HIS2 D 586 ASN2 D 599 ASN2 D 718 ASN
Page 27 Full wwPDB EM Model Validation Report 6M18
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○
Of 44 ligands modelled in this entry, 2 are monoatomic - leaving 42 for Mogul analysis.
In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are defined in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).
Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2
3 NAG A 701 1 14,14,15 0.53 0 17,19,21 0.45 03 NAG A 702 1 14,14,15 0.36 0 17,19,21 0.38 03 NAG A 703 1,3 14,14,15 0.82 1 (7%) 17,19,21 1.04 2 (11%)3 NAG A 704 3 14,14,15 0.51 0 17,19,21 0.37 03 NAG A 705 1 14,14,15 0.42 0 17,19,21 0.45 03 NAG A 706 1 14,14,15 0.42 0 17,19,21 0.73 1 (5%)4 3PH A 707 - 47,47,47 0.96 2 (4%) 51,52,52 1.11 3 (5%)4 3PH A 708 - 47,47,47 0.91 2 (4%) 51,52,52 1.13 3 (5%)3 NAG B 901 3,2 14,14,15 0.31 0 17,19,21 0.67 1 (5%)3 NAG B 902 3 14,14,15 0.24 0 17,19,21 0.57 03 NAG B 903 3,2 14,14,15 0.30 0 17,19,21 0.62 1 (5%)3 NAG B 904 3 14,14,15 0.27 0 17,19,21 0.51 03 NAG B 905 3,2 14,14,15 0.65 0 17,19,21 1.01 1 (5%)3 NAG B 906 3 14,14,15 0.22 0 17,19,21 0.64 1 (5%)3 NAG B 907 2 14,14,15 0.38 0 17,19,21 0.61 1 (5%)
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Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2
3 NAG B 908 3,2 14,14,15 0.38 0 17,19,21 0.56 03 NAG B 909 3 14,14,15 0.28 0 17,19,21 0.46 03 NAG B 910 3,2 14,14,15 0.24 0 17,19,21 0.56 03 NAG B 911 3 14,14,15 0.34 0 17,19,21 0.42 03 NAG B 912 3,2 14,14,15 0.31 0 17,19,21 0.60 03 NAG B 913 3 14,14,15 0.22 0 17,19,21 0.67 1 (5%)3 NAG C 701 1 14,14,15 0.53 0 17,19,21 0.45 03 NAG C 702 1 14,14,15 0.36 0 17,19,21 0.38 03 NAG C 703 1,3 14,14,15 0.82 1 (7%) 17,19,21 1.04 2 (11%)3 NAG C 704 3 14,14,15 0.51 0 17,19,21 0.37 03 NAG C 705 1 14,14,15 0.42 0 17,19,21 0.45 03 NAG C 706 1 14,14,15 0.42 0 17,19,21 0.73 1 (5%)4 3PH C 707 - 47,47,47 0.96 2 (4%) 51,52,52 1.11 3 (5%)4 3PH C 708 - 47,47,47 0.91 2 (4%) 51,52,52 1.13 3 (5%)3 NAG D 901 3,2 14,14,15 0.31 0 17,19,21 0.67 1 (5%)3 NAG D 902 3 14,14,15 0.24 0 17,19,21 0.57 03 NAG D 903 3,2 14,14,15 0.30 0 17,19,21 0.62 1 (5%)3 NAG D 904 3 14,14,15 0.27 0 17,19,21 0.51 03 NAG D 905 3,2 14,14,15 0.65 0 17,19,21 1.01 1 (5%)3 NAG D 906 3 14,14,15 0.22 0 17,19,21 0.64 1 (5%)3 NAG D 907 2 14,14,15 0.38 0 17,19,21 0.61 1 (5%)3 NAG D 908 3,2 14,14,15 0.38 0 17,19,21 0.56 03 NAG D 909 3 14,14,15 0.28 0 17,19,21 0.46 03 NAG D 910 3,2 14,14,15 0.24 0 17,19,21 0.56 03 NAG D 911 3 14,14,15 0.34 0 17,19,21 0.42 03 NAG D 912 3,2 14,14,15 0.31 0 17,19,21 0.60 03 NAG D 913 3 14,14,15 0.22 0 17,19,21 0.67 1 (5%)
In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.’-’ means no outliers of that kind were identified.
Mol Type Chain Res Link Chirals Torsions Rings3 NAG A 701 1 - 2/6/23/26 0/1/1/13 NAG A 702 1 - 0/6/23/26 0/1/1/13 NAG A 703 1,3 - 2/6/23/26 0/1/1/13 NAG A 704 3 - 2/6/23/26 0/1/1/13 NAG A 705 1 - 2/6/23/26 0/1/1/1
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Continued from previous page...Mol Type Chain Res Link Chirals Torsions Rings3 NAG A 706 1 - 0/6/23/26 0/1/1/14 3PH A 707 - - 18/49/49/49 -4 3PH A 708 - - 21/49/49/49 -3 NAG B 901 3,2 - 1/6/23/26 0/1/1/13 NAG B 902 3 - 0/6/23/26 0/1/1/13 NAG B 903 3,2 - 0/6/23/26 0/1/1/13 NAG B 904 3 - 2/6/23/26 0/1/1/13 NAG B 905 3,2 - 2/6/23/26 0/1/1/13 NAG B 906 3 - 1/6/23/26 0/1/1/13 NAG B 907 2 - 0/6/23/26 0/1/1/13 NAG B 908 3,2 - 1/6/23/26 0/1/1/13 NAG B 909 3 - 2/6/23/26 0/1/1/13 NAG B 910 3,2 - 2/6/23/26 0/1/1/13 NAG B 911 3 - 2/6/23/26 0/1/1/13 NAG B 912 3,2 - 2/6/23/26 0/1/1/13 NAG B 913 3 - 2/6/23/26 0/1/1/13 NAG C 701 1 - 2/6/23/26 0/1/1/13 NAG C 702 1 - 0/6/23/26 0/1/1/13 NAG C 703 1,3 - 2/6/23/26 0/1/1/13 NAG C 704 3 - 2/6/23/26 0/1/1/13 NAG C 705 1 - 2/6/23/26 0/1/1/13 NAG C 706 1 - 0/6/23/26 0/1/1/14 3PH C 707 - - 18/49/49/49 -4 3PH C 708 - - 21/49/49/49 -3 NAG D 901 3,2 - 1/6/23/26 0/1/1/13 NAG D 902 3 - 0/6/23/26 0/1/1/13 NAG D 903 3,2 - 0/6/23/26 0/1/1/13 NAG D 904 3 - 2/6/23/26 0/1/1/13 NAG D 905 3,2 - 2/6/23/26 0/1/1/13 NAG D 906 3 - 1/6/23/26 0/1/1/13 NAG D 907 2 - 0/6/23/26 0/1/1/13 NAG D 908 3,2 - 1/6/23/26 0/1/1/13 NAG D 909 3 - 2/6/23/26 0/1/1/13 NAG D 910 3,2 - 2/6/23/26 0/1/1/13 NAG D 911 3 - 2/6/23/26 0/1/1/13 NAG D 912 3,2 - 2/6/23/26 0/1/1/13 NAG D 913 3 - 2/6/23/26 0/1/1/1
Page 30 Full wwPDB EM Model Validation Report 6M18
All (10) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)4 A 707 3PH O31-C31 4.34 1.46 1.334 C 707 3PH O31-C31 4.34 1.46 1.334 A 707 3PH O21-C21 4.06 1.45 1.344 C 707 3PH O21-C21 4.06 1.45 1.344 A 708 3PH O21-C21 3.98 1.45 1.344 C 708 3PH O21-C21 3.98 1.45 1.344 A 708 3PH O31-C31 3.95 1.45 1.334 C 708 3PH O31-C31 3.95 1.45 1.333 C 703 NAG O5-C1 -2.86 1.39 1.433 A 703 NAG O5-C1 -2.86 1.39 1.43
All (30) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)4 A 708 3PH O21-C21-C22 4.34 120.98 111.514 C 708 3PH O21-C21-C22 4.34 120.98 111.514 A 707 3PH O21-C21-C22 3.93 120.09 111.514 C 707 3PH O21-C21-C22 3.93 120.09 111.514 A 707 3PH O31-C31-C32 3.10 121.89 111.934 C 707 3PH O31-C31-C32 3.10 121.89 111.933 D 905 NAG C1-O5-C5 3.06 116.36 112.203 B 905 NAG C1-O5-C5 3.06 116.36 112.203 C 706 NAG C1-O5-C5 2.68 115.85 112.203 A 706 NAG C1-O5-C5 2.68 115.85 112.204 A 708 3PH O31-C31-C32 2.66 120.48 111.934 C 708 3PH O31-C31-C32 2.66 120.48 111.934 A 708 3PH C2-O21-C21 -2.49 111.60 117.824 C 708 3PH C2-O21-C21 -2.49 111.60 117.823 B 913 NAG C1-O5-C5 2.35 115.39 112.203 D 913 NAG C1-O5-C5 2.35 115.39 112.203 D 906 NAG C1-O5-C5 2.26 115.28 112.203 B 906 NAG C1-O5-C5 2.26 115.28 112.203 C 703 NAG O4-C4-C5 -2.21 103.77 109.293 A 703 NAG O4-C4-C5 -2.21 103.77 109.293 B 907 NAG C1-O5-C5 2.13 115.10 112.203 D 907 NAG C1-O5-C5 2.13 115.10 112.204 A 707 3PH C2-O21-C21 -2.05 112.69 117.824 C 707 3PH C2-O21-C21 -2.05 112.69 117.823 C 703 NAG C4-C3-C2 2.04 114.01 111.023 A 703 NAG C4-C3-C2 2.04 114.01 111.023 D 903 NAG C1-O5-C5 2.03 114.96 112.203 B 903 NAG C1-O5-C5 2.03 114.96 112.20
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Page 31 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)3 D 901 NAG C1-O5-C5 2.03 114.96 112.203 B 901 NAG C1-O5-C5 2.03 114.96 112.20
There are no chirality outliers.
All (128) torsion outliers are listed below:
Mol Chain Res Type Atoms4 A 708 3PH C1-O11-P-O134 A 708 3PH C1-O11-P-O144 C 708 3PH C1-O11-P-O134 C 708 3PH C1-O11-P-O144 A 707 3PH C1-O11-P-O134 A 707 3PH C1-O11-P-O124 C 707 3PH C1-O11-P-O134 C 707 3PH C1-O11-P-O123 D 911 NAG O5-C5-C6-O63 B 913 NAG O5-C5-C6-O63 B 911 NAG O5-C5-C6-O63 D 913 NAG O5-C5-C6-O63 B 910 NAG O5-C5-C6-O63 D 910 NAG O5-C5-C6-O63 B 904 NAG O5-C5-C6-O63 D 904 NAG O5-C5-C6-O63 C 703 NAG C4-C5-C6-O63 A 703 NAG C4-C5-C6-O63 D 911 NAG C4-C5-C6-O63 B 913 NAG C4-C5-C6-O63 B 911 NAG C4-C5-C6-O63 D 913 NAG C4-C5-C6-O63 D 905 NAG C4-C5-C6-O63 B 909 NAG C4-C5-C6-O63 B 905 NAG C4-C5-C6-O63 D 909 NAG C4-C5-C6-O63 C 703 NAG O5-C5-C6-O63 A 703 NAG O5-C5-C6-O63 D 905 NAG O5-C5-C6-O63 B 905 NAG O5-C5-C6-O63 C 704 NAG C4-C5-C6-O63 A 704 NAG C4-C5-C6-O63 B 904 NAG C4-C5-C6-O63 D 904 NAG C4-C5-C6-O64 A 707 3PH C32-C31-O31-C3
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Continued from previous page...Mol Chain Res Type Atoms4 C 707 3PH C32-C31-O31-C33 B 910 NAG C4-C5-C6-O63 D 910 NAG C4-C5-C6-O63 C 705 NAG O5-C5-C6-O63 A 705 NAG O5-C5-C6-O63 C 704 NAG O5-C5-C6-O63 A 704 NAG O5-C5-C6-O64 A 707 3PH O32-C31-O31-C34 C 707 3PH O32-C31-O31-C33 A 701 NAG O5-C5-C6-O63 C 701 NAG O5-C5-C6-O63 C 705 NAG C4-C5-C6-O63 A 705 NAG C4-C5-C6-O63 B 909 NAG O5-C5-C6-O63 D 909 NAG O5-C5-C6-O64 A 707 3PH C35-C36-C37-C384 C 707 3PH C35-C36-C37-C383 B 912 NAG C4-C5-C6-O63 D 912 NAG C4-C5-C6-O64 A 707 3PH C26-C27-C28-C294 A 707 3PH C3D-C3E-C3F-C3G4 C 707 3PH C26-C27-C28-C294 C 707 3PH C3D-C3E-C3F-C3G4 A 708 3PH C22-C21-O21-C24 C 708 3PH C22-C21-O21-C24 A 708 3PH C21-C22-C23-C244 C 708 3PH C21-C22-C23-C244 A 708 3PH C36-C37-C38-C394 C 708 3PH C36-C37-C38-C394 A 708 3PH C31-C32-C33-C344 C 708 3PH C31-C32-C33-C344 A 708 3PH C28-C29-C2A-C2B4 C 708 3PH C28-C29-C2A-C2B4 A 708 3PH O22-C21-O21-C24 C 708 3PH O22-C21-O21-C24 A 707 3PH O21-C2-C3-O314 C 707 3PH O21-C2-C3-O314 A 708 3PH C2E-C2F-C2G-C2H4 C 708 3PH C2E-C2F-C2G-C2H4 A 707 3PH C3E-C3F-C3G-C3H4 C 707 3PH C3E-C3F-C3G-C3H4 A 708 3PH C1-O11-P-O12
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Continued from previous page...Mol Chain Res Type Atoms4 C 708 3PH C1-O11-P-O124 A 707 3PH C24-C25-C26-C274 C 707 3PH C24-C25-C26-C273 B 912 NAG O5-C5-C6-O63 D 912 NAG O5-C5-C6-O64 A 707 3PH C25-C26-C27-C284 C 707 3PH C25-C26-C27-C284 A 707 3PH C3B-C3C-C3D-C3E4 C 707 3PH C3B-C3C-C3D-C3E4 A 707 3PH C1-C2-C3-O314 C 707 3PH C1-C2-C3-O313 A 701 NAG C4-C5-C6-O63 C 701 NAG C4-C5-C6-O64 A 708 3PH C3B-C3C-C3D-C3E4 C 708 3PH C3B-C3C-C3D-C3E3 D 901 NAG C4-C5-C6-O63 B 901 NAG C4-C5-C6-O64 A 708 3PH C3D-C3E-C3F-C3G4 C 708 3PH C3D-C3E-C3F-C3G4 A 708 3PH O11-C1-C2-C34 C 708 3PH O11-C1-C2-C34 A 707 3PH C32-C33-C34-C354 C 707 3PH C32-C33-C34-C354 A 708 3PH O11-C1-C2-O214 C 708 3PH O11-C1-C2-O214 A 708 3PH O21-C2-C3-O314 C 708 3PH O21-C2-C3-O314 A 707 3PH C22-C23-C24-C254 C 707 3PH C22-C23-C24-C254 A 708 3PH C33-C34-C35-C364 C 708 3PH C33-C34-C35-C364 A 708 3PH C1-C2-C3-O314 C 708 3PH C1-C2-C3-O314 A 707 3PH C31-C32-C33-C344 C 707 3PH C31-C32-C33-C344 A 708 3PH C29-C2A-C2B-C2C4 C 708 3PH C29-C2A-C2B-C2C4 A 708 3PH C32-C33-C34-C354 C 708 3PH C32-C33-C34-C354 A 707 3PH C1-O11-P-O144 C 707 3PH C1-O11-P-O144 A 707 3PH C3F-C3G-C3H-C3I
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Page 34 Full wwPDB EM Model Validation Report 6M18
Continued from previous page...Mol Chain Res Type Atoms4 C 707 3PH C3F-C3G-C3H-C3I3 D 908 NAG C4-C5-C6-O63 B 908 NAG C4-C5-C6-O64 A 708 3PH C25-C26-C27-C284 C 708 3PH C25-C26-C27-C284 A 708 3PH C34-C35-C36-C374 C 708 3PH C34-C35-C36-C373 D 906 NAG C4-C5-C6-O63 B 906 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 A 708 3PH 1 0
The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identified as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identified by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identified rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not find sufficientequivalents in the CSD to analyse the geometry.
Ligand 3PH A 707
Bond lengths Bond angles
Torsions Rings
Page 35 Full wwPDB EM Model Validation Report 6M18
Ligand 3PH A 708
Bond lengths Bond angles
Torsions Rings
Ligand 3PH C 707
Bond lengths Bond angles
Torsions Rings
Ligand 3PH C 708
Bond lengths Bond angles
Torsions Rings
5.7 Other polymers i○
There are no such residues in this entry.
Page 36 Full wwPDB EM Model Validation Report 6M18
5.8 Polymer linkage issues i○
There are no chain breaks in this entry.