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Full wwPDB/EMDataBank EM Map/Model ValidationReport iO
Mar 17, 2018 � 01:38 PM EDT
PDB ID : 5T4QEMDB ID: : EMD-8359
Title : Autoinhibited E. coli ATP synthase state 3Authors : Sobti, M.; Smits, C.; Wong, A.S.W.; Ishmukhametov, R.; Stock, D.; Sandin,
S.; Stewart, A.G.Deposited on : 2016-08-29Resolution : 8.53 Å(reported)
This is a Full wwPDB/EMDataBank EM Map/Model Validation Reportfor a publicly released PDB/EMDB entry.
We welcome your comments at validation@mail.wwpdb.orgA user guide is available at
https://www.wwpdb.org/validation/2017/EMValidationReportHelpwith speci�c help available everywhere you see the iO symbol.
MolProbity : 4.02b-467Mogul : 1.7.3 (157068), CSD as539be (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) : rb-20031021
Page 2 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
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 8.53 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 136327 1886Ramachandran outliers 132723 1663
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 513
1 B 513
1 C 513
2 D 471
2 E 471
2 F 471
3 G 287
4 H 139
5 I 155
5 J 155
6 K 271Continued on next page...
Page 3 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
Continued from previous page...
Mol Chain Length Quality of chain
7 L 177
8 M 79
8 N 79
8 O 79
8 P 79
8 Q 79
8 R 79
8 S 79
8 T 79
8 U 79
8 V 79
Page 4 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
2 Entry composition iO
There are 10 unique types of molecules in this entry. The entry contains 23568 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 ATP synthase subunit alpha.
Mol Chain Residues Atoms AltConf Trace
1 A 511Total C N O2507 1485 511 511
0 0
1 B 510Total C N O2502 1482 510 510
0 0
1 C 508Total C N O2492 1476 508 508
0 0
There are 15 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA 47 ALA CYS con�ict UNP B7MGF4A 90 ALA CYS con�ict UNP B7MGF4A 193 ALA CYS con�ict UNP B7MGF4A 243 ALA CYS con�ict UNP B7MGF4A 419 ASN LYS con�ict UNP B7MGF4B 47 ALA CYS con�ict UNP B7MGF4B 90 ALA CYS con�ict UNP B7MGF4B 193 ALA CYS con�ict UNP B7MGF4B 243 ALA CYS con�ict UNP B7MGF4B 419 ASN LYS con�ict UNP B7MGF4C 47 ALA CYS con�ict UNP B7MGF4C 90 ALA CYS con�ict UNP B7MGF4C 193 ALA CYS con�ict UNP B7MGF4C 243 ALA CYS con�ict UNP B7MGF4C 419 ASN LYS con�ict UNP B7MGF4
� Molecule 2 is a protein called ATP synthase subunit beta.
Mol Chain Residues Atoms AltConf Trace
2 D 466Total C N O2284 1352 466 466
0 0
2 E 466Total C N O2284 1352 466 466
0 0
Continued on next page...
Page 5 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
Continued from previous page...
Mol Chain Residues Atoms AltConf Trace
2 F 466Total C N O2284 1352 466 466
0 0
There are 36 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceD -11 MET - expression tag UNP B7MGF2D -10 ARG - expression tag UNP B7MGF2D -9 GLY - expression tag UNP B7MGF2D -8 SER - expression tag UNP B7MGF2D -7 HIS - expression tag UNP B7MGF2D -6 HIS - expression tag UNP B7MGF2D -5 HIS - expression tag UNP B7MGF2D -4 HIS - expression tag UNP B7MGF2D -3 HIS - expression tag UNP B7MGF2D -2 HIS - expression tag UNP B7MGF2D -1 GLY - expression tag UNP B7MGF2D 137 ALA CYS con�ict UNP B7MGF2E -11 MET - expression tag UNP B7MGF2E -10 ARG - expression tag UNP B7MGF2E -9 GLY - expression tag UNP B7MGF2E -8 SER - expression tag UNP B7MGF2E -7 HIS - expression tag UNP B7MGF2E -6 HIS - expression tag UNP B7MGF2E -5 HIS - expression tag UNP B7MGF2E -4 HIS - expression tag UNP B7MGF2E -3 HIS - expression tag UNP B7MGF2E -2 HIS - expression tag UNP B7MGF2E -1 GLY - expression tag UNP B7MGF2E 137 ALA CYS con�ict UNP B7MGF2F -11 MET - expression tag UNP B7MGF2F -10 ARG - expression tag UNP B7MGF2F -9 GLY - expression tag UNP B7MGF2F -8 SER - expression tag UNP B7MGF2F -7 HIS - expression tag UNP B7MGF2F -6 HIS - expression tag UNP B7MGF2F -5 HIS - expression tag UNP B7MGF2F -4 HIS - expression tag UNP B7MGF2F -3 HIS - expression tag UNP B7MGF2F -2 HIS - expression tag UNP B7MGF2F -1 GLY - expression tag UNP B7MGF2F 137 ALA CYS con�ict UNP B7MGF2
Page 6 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
� Molecule 3 is a protein called ATP synthase gamma chain.
Mol Chain Residues Atoms AltConf Trace
3 G 284Total C N O1400 832 284 284
0 0
There are 3 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceG 5 ASP GLU con�ict UNP B7MGF3G 87 ALA CYS con�ict UNP B7MGF3G 112 ALA CYS con�ict UNP B7MGF3
� Molecule 4 is a protein called ATP synthase epsilon chain.
Mol Chain Residues Atoms AltConf Trace
4 H 136Total C N O668 396 136 136
0 0
� Molecule 5 is a protein called ATP synthase subunit b.
Mol Chain Residues Atoms AltConf Trace
5 I 155Total C N O772 462 155 155
0 0
5 J 155Total C N O772 462 155 155
0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceI 21 ALA CYS con�ict UNP P0ABA2J 21 ALA CYS con�ict UNP P0ABA2
� Molecule 6 is a protein called ATP synthase subunit a.
Mol Chain Residues Atoms AltConf Trace
6 K 211Total C N O1040 618 211 211
0 0
� Molecule 7 is a protein called ATP synthase subunit delta.
Page 7 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
Mol Chain Residues Atoms AltConf Trace
7 L 160Total C N O793 473 160 160
0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceL 64 ALA CYS con�ict UNP B7MGF5L 140 ALA CYS con�ict UNP B7MGF5
� Molecule 8 is a protein called ATP synthase subunit c.
Mol Chain Residues Atoms AltConf Trace
8 M 75Total C N O365 215 75 75
0 0
8 N 75Total C N O365 215 75 75
0 0
8 O 75Total C N O365 215 75 75
0 0
8 P 75Total C N O365 215 75 75
0 0
8 Q 75Total C N O365 215 75 75
0 0
8 R 75Total C N O365 215 75 75
0 0
8 S 75Total C N O365 215 75 75
0 0
8 T 75Total C N O365 215 75 75
0 0
8 U 75Total C N O365 215 75 75
0 0
8 V 75Total C N O365 215 75 75
0 0
� Molecule 9 is ADENOSINE-5'-TRIPHOSPHATE (three-letter code: ATP) (formula:C10H16N5O13P3).
Page 8 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
Mol Chain Residues Atoms AltConf
9 A 1Total C N O P31 10 5 13 3
0
9 B 1Total C N O P31 10 5 13 3
0
9 C 1Total C N O P31 10 5 13 3
0
� Molecule 10 is ADENOSINE-5'-DIPHOSPHATE (three-letter code: ADP) (formula:C10H15N5O10P2).
Page 9 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
Mol Chain Residues Atoms AltConf
10 D 1Total C N O P27 10 5 10 2
0
Page 10 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
3 Residue-property plots iO
These plots are drawn for all protein, RNA and DNA chains in the entry. The �rst 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: ATP synthase subunit alpha
Chain A:
M1
I31
V32
I41
I53
S54
L55
Y60
D69
P114
P120
V129
V136
I137
G149
N185
S189
T204
I205
V208
V209
L212
E213
G216
A232
Y236
A243
E247
P281
P287
E310
A311
K314
G315
G319
T343
S347
N358
A362
R394
A398
P438
S445
L446
V447
L448
F449
A450
A451
K463
F467
A470
Y474
M483
Q484
N487
Q488
I496
E497
L500
K501
L504
Q511
SER
TRP
• Molecule 1: ATP synthase subunit alpha
Chain B:
MET
Q2
S5
L11
R15
V22
I31
L55
G85
M86
K87
V88
V97
P120
F126
P134
T148
G149
L178
I198
L237
A241
A256
R279
P280
P281
G282
P287
L324
L327
T343
S347
R394
A398
Q399
Y400
R401
E402
L403
A404
D422
K426
Q443
V447
G454
G465
A469
A473
I496
L500
L504
D505
K508
A509
T510
Q511
SER
TRP
• Molecule 1: ATP synthase subunit alpha
Chain C:
MET
GLN
LEU
N4
I8
S9
E10
N27
L44
L55
G85
V97
A113
P114
I115
D116
G117
P120
F126
I157
G174
L178
I191
V209
E213
R279
P280
P281
G282
P287
V337
T343
S347
P370
V377
G378
T395
Q399
Y400
L403
A404
D414
Q443
Q444
V447
L448
G454
I464
E468
L472
A473
D476
R477
P481
I496
L500
I503
L504
D505
S506
F507
K508
A509
T510
Q511
SER
TRP
• Molecule 2: ATP synthase subunit beta
Chain D:
MET
ARG
GLY
SER
HIS
H-6
H-5
H-4
H-3
M0
G10
F17
P18
E30
N33
V42
T53
S59
G65
D70
P74
V77
P78
V90
L91
G92
E93
A113
V132
M136
A137
P138
V153
I163
A167
V175
E192
S196
P212
G223
A227
R231
D242
R246
A250
P262
V277
R281
A295
D305
P308
F312
Y331
P332
D345
P346
V349
K371
A375
F404
F405
V406
A407
P439
A452
A456
L459
• Molecule 2: ATP synthase subunit beta
Page 11 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
Chain E:
MET
ARG
GLY
SER
HIS
H-6
H-5
H-4
H-3
F17
P23
G65
E93
S120
N121
T128
G129
V157
N158
E161
L162
E185
F189
M193
D200
K201
E211
G214
R218
V219
A220
L221
T222
G223
L224
T225
M226
R246
A250
P262
V298
D305
P306
P336
D345
P346
V349
G350
Y354
G359
I363
Y367
E385
V389
A393
R394
K395
I396
Q397
R398
F399
V418
T423
I424
F427
K428
G429
G433
D436
L459
• Molecule 2: ATP synthase subunit beta
Chain F:
MET
ARG
GLY
SER
HIS
H-6
H-3
V6
Q7
V8
F17
P23
L71
P78
V79
G85
E93
P94
A113
P114
E117
S120
L125
A140
G149
V157
N158
E161
L162
G178
Y206
P212
P213
L221
T222
G223
L224
T225
M226
A227
L238
R246
A250
G251
T252
S255
A256
P262
E274
M275
L278
Q279
T285
T291
P306
A309
T310
A313
H314
L321
D345
V349
I363
Y367
E385
V389
P414
G433
P439
L459
• Molecule 3: ATP synthase gamma chain
Chain G:
MET
A1
K4
Q35
A39
R42
I52
A56
D71
R74
I92
K96
E101
M102
K103
T104
W105
T106
D107
K108
G109
V110
Q111
P151
M155
G162
K173
V181
P182
P189
E208
P209
D210
P211
K212
D216
R220
E224
S225
Y228
Q229
E233
S237
A245
A249
I279
A283
A284
ALA
VAL
• Molecule 4: ATP synthase epsilon chain
Chain H:
MET
A1
H5
L19
Y35
P36
L42
K46
L69
Q72
L89
R93
E96
A97
K100
A101
A119
E120
K123
A124
K136
ALA
MET
• Molecule 5: ATP synthase subunit b
Chain I:
N2
I7
A11
I12
A13
L16
F17
F20
A21
V25
P28
A32
S139
A143
L156
• Molecule 5: ATP synthase subunit b
Chain J:
N2
I7
A11
P27
A31
E34
K35
K38
E39
D42
S46
A50
V124
A125
A128
V129
D150
A154
E155
L156
• Molecule 6: ATP synthase subunit a
Page 12 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
Chain K:
MET
ALA
SER
GLU
ASN
MET
THR
PRO
GLN
ASP
TYR
ILE
GLY
HIS
HIS
LEU
ASN
ASN
LEU
GLN
LEU
ASP
LEU
ARG
THR
PHE
SER
LEU
VAL
ASP
PRO
GLN
ASN
PRO
PRO
ALA
THR
PHE
TRP
THR
ILE
ASN
ILE
ASP
SER
M46
V51
L55
K74
F75
S98
I101
A102
P103
L104
T107
I108
W111
V112
M115
N116
L121
L126
P127
TYR
ILE
ALA
GLU
HIS
VAL
LEU
GLY
LEU
PRO
ALA
LEU
R140
V141
V142
P143
D146
T150
A154
F158
L162
I171
G172
Q181
H185
W186
A187
G197
V198
L201
S202
V205
L209
L229
P230
S268
GLU
GLU
HIS
• Molecule 7: ATP synthase subunit delta
Chain L:
MET
SER
E2
F3
I4
P9
A13
Q28
L31
A32
A35
E36
Q42
L46
T55
E58
S59
A62
V63
Q94
F95
I96
H97
L98
R99
A100
I124
S125
A126
A127
M128
E129
K130
R131
L132
A148
G149
I152
R153
M157
G161
SER
VAL
ARG
GLY
ARG
LEU
GLU
ARG
LEU
ALA
ASP
VAL
LEU
GLN
SER
• Molecule 8: ATP synthase subunit c
Chain M:
MET
GLU
N3
L4
L8
A12
M16
I22
G23
F35
A39
P47
I63
Y73
A77
VAL
ALA
• Molecule 8: ATP synthase subunit c
Chain N:
MET
GLU
N3
L4
L8
I22
G23
F35
A39
P43
P47
I63
Y73
A77
VAL
ALA
• Molecule 8: ATP synthase subunit c
Chain O:
MET
GLU
N3
L4
L8
I22
I46
P47
I63
Y73
A77
VAL
ALA
• Molecule 8: ATP synthase subunit c
Chain P:
MET
GLU
N3
L4
L8
G23
I46
P47
I63
Y73
A77
VAL
ALA
• Molecule 8: ATP synthase subunit c
Page 13 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
Chain Q:
MET
GLU
N3
L4
L8
A12
M16
I22
G23
P47
I63
Y73
A77
VAL
ALA
• Molecule 8: ATP synthase subunit c
Chain R:
MET
GLU
N3
L4
L8
A12
M16
I22
G23
F35
A39
P43
P47
I63
Y73
A77
VAL
ALA
• Molecule 8: ATP synthase subunit c
Chain S:
MET
GLU
N3
L4
L8
A12
M16
I22
G23
F35
A39
P43
P47
I63
Y73
A77
VAL
ALA
• Molecule 8: ATP synthase subunit c
Chain T:
MET
GLU
N3
L4
L8
A12
M16
I22
G23
F35
A39
P43
P47
I63
Y73
A77
VAL
ALA
• Molecule 8: ATP synthase subunit c
Chain U:
MET
GLU
N3
L4
L8
I22
G23
F35
A39
P43
P47
I63
Y73
A77
VAL
ALA
• Molecule 8: ATP synthase subunit c
Chain V:
MET
GLU
N3
L4
L8
A12
M16
I22
G23
F35
A39
P43
P47
I63
Y73
A77
VAL
ALA
Page 14 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
4 Experimental information iO
Property Value SourceReconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, Not provided DepositorNumber of particles used 95345 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) 29 Depositor
Minimum defocus (nm) Not provided DepositorMaximum defocus (nm) Not provided DepositorMagni�cation Not provided DepositorImage detector FEI FALCON II (4k x 4k) Depositor
Page 15 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
5 Model quality iO
5.1 Standard geometry iO
Bond lengths and bond angles in the following residue types are not validated in this section: ATP,ADP
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| >2 RMSZ #|Z| >2
1 A 0.25 0/2506 0.43 0/34781 B 0.25 0/2501 0.43 0/34711 C 0.24 0/2491 0.43 0/34572 D 0.24 0/2283 0.42 0/31672 E 0.24 0/2283 0.43 0/31672 F 0.25 0/2283 0.45 0/31673 G 0.23 0/1399 0.39 0/19454 H 0.27 0/667 0.45 0/9255 I 0.23 0/771 0.33 0/10765 J 0.23 0/771 0.34 0/10766 K 0.23 0/1038 0.41 0/14417 L 0.23 0/792 0.39 0/11038 M 0.23 0/364 0.34 0/5028 N 0.24 0/364 0.34 0/5028 O 0.23 0/364 0.33 0/5028 P 0.23 0/364 0.34 0/5028 Q 0.24 0/364 0.34 0/5028 R 0.23 0/364 0.34 0/5028 S 0.24 0/364 0.34 0/5028 T 0.23 0/364 0.34 0/5028 U 0.24 0/364 0.34 0/5028 V 0.23 0/364 0.34 0/502All All 0.24 0/23425 0.41 0/32493
There are no bond length outliers.
There are no bond angle outliers.
There are no chirality outliers.
There are no planarity outliers.
Page 16 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
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 2507 0 1240 23 01 B 2502 0 1235 20 01 C 2492 0 1231 20 02 D 2284 0 1065 16 02 E 2284 0 1065 24 02 F 2284 0 1065 23 03 G 1400 0 665 17 04 H 668 0 330 8 05 I 772 0 406 9 05 J 772 0 406 11 06 K 1040 0 464 18 07 L 793 0 407 17 08 M 365 0 192 7 08 N 365 0 192 5 08 O 365 0 192 3 08 P 365 0 192 3 08 Q 365 0 192 5 08 R 365 0 192 6 08 S 365 0 192 6 08 T 365 0 192 7 08 U 365 0 192 5 08 V 365 0 192 7 09 A 31 0 12 0 09 B 31 0 12 0 09 C 31 0 12 0 010 D 27 0 12 0 0All All 23568 0 11547 251 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 7.
All (251) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
2:E:128:THR:H 2:E:129:GLY:HA2 1.55 0.71Continued on next page...
Page 17 Full wwPDB/EMDataBank EM Map/Model Validation Report 5T4Q
Continued from previous page...
Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
7:L:58:GLU:O 7:L:62:ALA:HB3 1.91 0.711:C:97:VAL:O 1:C:126:PHE:HA 1.91 0.711:A:53:ILE:O 1:A:60:TYR:HA 1.91 0.715:J:124:VAL:O 5:J:128:ALA:HB3 1.94 0.685:J:27:PRO:O 5:J:31:ALA:HB3 1.92 0.68
2:F:238:LEU:HA 2:F:291:THR:O 1.94 0.671:B:237:LEU:O 1:B:241:ALA:HB3 1.96 0.656:K:186:TRP:H 6:K:187:ALA:C 2.00 0.651:A:446:LEU:O 1:A:450:ALA:HB3 2.00 0.622:F:309:ALA:O 2:F:313:ALA:HB3 2.00 0.622:D:371:LYS:O 2:D:375:ALA:HB3 1.99 0.612:F:178:GLY:O 2:F:206:TYR:HA 2.00 0.611:B:400:TYR:O 1:B:404:ALA:HB3 2.02 0.594:H:42:LEU:HA 4:H:69:LEU:O 2.03 0.581:A:394:ARG:O 1:A:398:ALA:HB3 2.03 0.585:I:139:SER:O 5:I:143:ALA:HB2 2.04 0.582:E:246:ARG:O 2:E:250:ALA:HB3 2.03 0.571:B:31:ILE:H 1:B:87:LYS:HA 1.71 0.567:L:9:PRO:O 7:L:13:ALA:HB3 2.07 0.552:E:128:THR:N 2:E:129:GLY:HA2 2.20 0.558:S:73:TYR:HA 8:S:77:ALA:HB3 1.90 0.545:J:150:ASP:O 5:J:154:ALA:HB3 2.07 0.548:Q:73:TYR:HA 8:Q:77:ALA:HB3 1.90 0.544:H:120:GLU:O 4:H:124:ALA:HB3 2.08 0.543:G:52:ILE:O 3:G:56:ALA:HB2 2.08 0.53
8:M:73:TYR:HA 8:M:77:ALA:HB3 1.90 0.538:U:73:TYR:HA 8:U:77:ALA:HB3 1.90 0.532:F:246:ARG:O 2:F:250:ALA:HB3 2.09 0.537:L:31:LEU:O 7:L:35:ALA:HB3 2.07 0.538:N:73:TYR:HA 8:N:77:ALA:HB3 1.90 0.538:V:73:TYR:HA 8:V:77:ALA:HB3 1.90 0.532:D:246:ARG:O 2:D:250:ALA:HB3 2.09 0.533:G:279:ILE:HA 3:G:283:ALA:HB3 1.90 0.521:B:256:ALA:O 1:B:324:LEU:HA 2.09 0.528:R:73:TYR:HA 8:R:77:ALA:HB3 1.90 0.528:O:73:TYR:HA 8:O:77:ALA:HB3 1.91 0.528:P:73:TYR:HA 8:P:77:ALA:HB3 1.91 0.521:B:97:VAL:O 1:B:126:PHE:HA 2.10 0.523:G:245:ALA:O 3:G:249:ALA:HB3 2.09 0.526:K:74:LYS:H 6:K:75:PHE:HA 1.75 0.511:A:447:VAL:O 1:A:451:ALA:HB3 2.11 0.51
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
8:P:23:GLY:HA3 8:Q:22:ILE:HA 1.93 0.514:H:97:ALA:O 4:H:101:ALA:HB3 2.11 0.518:T:73:TYR:HA 8:T:77:ALA:HB3 1.91 0.501:A:358:ASN:O 1:A:362:ALA:HB2 2.12 0.491:B:394:ARG:O 1:B:398:ALA:HB3 2.11 0.498:N:23:GLY:HA3 8:O:22:ILE:HA 1.94 0.494:H:5:HIS:HA 4:H:19:LEU:HA 1.95 0.491:B:465:GLY:O 1:B:469:ALA:HB3 2.13 0.488:S:23:GLY:HA3 8:T:22:ILE:HA 1.94 0.481:C:27:ASN:HA 1:C:44:LEU:HA 1.94 0.481:A:243:ALA:O 1:A:247:GLU:CB 2.62 0.481:C:116:ASP:HA 1:C:117:GLY:HA2 1.53 0.488:M:22:ILE:HA 8:V:23:GLY:HA3 1.96 0.481:C:400:TYR:O 1:C:404:ALA:HB3 2.13 0.472:E:200:ASP:HA 2:E:201:LYS:HA 1.53 0.478:Q:23:GLY:HA3 8:R:22:ILE:HA 1.95 0.472:D:-4:HIS:HA 2:D:-3:HIS:C 2.34 0.475:J:124:VAL:O 5:J:128:ALA:CB 2.62 0.477:L:42:GLN:O 7:L:46:LEU:CB 2.63 0.472:E:363:ILE:O 2:E:367:TYR:CB 2.63 0.475:J:7:ILE:O 5:J:11:ALA:HB3 2.14 0.47
8:U:23:GLY:HA3 8:V:22:ILE:HA 1.96 0.477:L:96:ILE:O 7:L:100:ALA:HB3 2.15 0.47
7:L:128:MET:O 7:L:132:LEU:CB 2.63 0.472:E:423:THR:O 2:E:427:PHE:CB 2.62 0.476:K:171:ILE:HA 6:K:172:GLY:HA3 1.69 0.462:D:163:ILE:O 2:D:167:ALA:HB3 2.16 0.462:F:310:THR:O 2:F:314:HIS:CB 2.64 0.466:K:74:LYS:N 6:K:75:PHE:HA 2.30 0.465:I:17:PHE:O 5:I:21:ALA:CB 2.64 0.465:I:28:PRO:O 5:I:32:ALA:HB3 2.16 0.46
1:A:314:LYS:HA 1:A:315:GLY:HA2 1.66 0.462:E:222:THR:O 2:E:226:MET:CB 2.64 0.465:J:38:LYS:O 5:J:42:ASP:CB 2.63 0.467:L:55:THR:O 7:L:59:SER:CB 2.63 0.466:K:111:TRP:O 6:K:115:MET:CB 2.64 0.462:E:424:ILE:O 2:E:428:LYS:CB 2.64 0.453:G:173:LYS:H 3:G:182:PRO:HA 1.81 0.452:D:227:ALA:O 2:D:231:ARG:CB 2.64 0.455:J:34:GLU:O 5:J:38:LYS:CB 2.65 0.455:I:16:LEU:O 5:I:20:PHE:CB 2.64 0.45
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:B:496:ILE:O 1:B:500:LEU:CB 2.65 0.452:E:395:LYS:O 2:E:399:PHE:CB 2.65 0.452:D:452:ALA:O 2:D:456:ALA:HB3 2.16 0.452:E:-4:HIS:HA 2:E:-3:HIS:HA 1.49 0.455:I:7:ILE:O 5:I:11:ALA:HB3 2.16 0.45
1:B:469:ALA:O 1:B:473:ALA:HB3 2.17 0.446:K:154:ALA:O 6:K:158:PHE:CB 2.65 0.446:K:198:VAL:O 6:K:202:SER:CB 2.65 0.441:A:497:GLU:O 1:A:501:LYS:CB 2.66 0.442:F:125:LEU:HA 2:F:140:ALA:HA 1.99 0.443:G:35:GLN:O 3:G:39:ALA:CB 2.66 0.441:C:157:ILE:HA 1:C:378:GLY:HA2 1.99 0.442:E:129:GLY:HA3 2:E:418:VAL:H 1.82 0.442:F:221:LEU:O 2:F:225:THR:CB 2.66 0.442:E:359:GLY:O 2:E:363:ILE:CB 2.66 0.441:C:468:GLU:O 1:C:472:LEU:CB 2.66 0.443:G:71:ASP:H 3:G:162:GLY:HA2 1.82 0.448:V:12:ALA:O 8:V:16:MET:CB 2.65 0.443:G:101:GLU:O 3:G:105:TRP:CB 2.65 0.443:G:220:ARG:O 3:G:224:GLU:CB 2.66 0.448:R:23:GLY:HA3 8:S:22:ILE:HA 2.00 0.441:A:232:ALA:O 1:A:236:TYR:CB 2.66 0.445:J:42:ASP:O 5:J:46:SER:CB 2.66 0.447:L:28:GLN:O 7:L:32:ALA:HB3 2.18 0.442:D:42:VAL:HA 2:D:53:THR:HA 1.99 0.443:G:225:SER:O 3:G:229:GLN:CB 2.66 0.446:K:158:PHE:O 6:K:162:LEU:CB 2.66 0.446:K:205:VAL:O 6:K:209:LEU:CB 2.66 0.447:L:149:GLY:O 7:L:153:ARG:CB 2.66 0.442:E:189:PHE:O 2:E:193:MET:CB 2.66 0.438:M:12:ALA:O 8:M:16:MET:CB 2.65 0.438:S:4:LEU:O 8:S:8:LEU:CB 2.66 0.43
1:C:399:GLN:O 1:C:403:LEU:CB 2.66 0.431:C:395:THR:O 1:C:399:GLN:CB 2.67 0.431:C:473:ALA:O 1:C:477:ARG:CB 2.66 0.438:U:4:LEU:O 8:U:8:LEU:CB 2.65 0.431:A:445:SER:O 1:A:449:PHE:CB 2.67 0.432:D:242:ASP:HA 2:D:295:ALA:HB3 2.00 0.432:F:252:THR:O 2:F:256:ALA:HB3 2.18 0.432:E:221:LEU:O 2:E:225:THR:CB 2.66 0.438:M:23:GLY:HA3 8:N:22:ILE:HA 2.01 0.43
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
2:E:350:GLY:O 2:E:354:TYR:CB 2.67 0.432:E:394:ARG:O 2:E:398:ARG:CB 2.67 0.432:F:223:GLY:O 2:F:227:ALA:HB3 2.18 0.438:M:35:PHE:O 8:M:39:ALA:CB 2.66 0.431:B:465:GLY:O 1:B:469:ALA:CB 2.67 0.431:C:496:ILE:O 1:C:500:LEU:CB 2.67 0.438:N:4:LEU:O 8:N:8:LEU:CB 2.66 0.438:V:4:LEU:O 8:V:8:LEU:CB 2.67 0.431:C:472:LEU:O 1:C:476:ASP:CB 2.67 0.432:D:308:PRO:O 2:D:312:PHE:CB 2.67 0.433:G:173:LYS:CB 3:G:181:VAL:O 2.67 0.434:H:93:ARG:O 4:H:97:ALA:HB3 2.19 0.431:A:343:THR:O 1:A:347:SER:CB 2.67 0.422:D:30:GLU:H 2:D:70:ASP:HA 1.84 0.423:G:224:GLU:O 3:G:228:TYR:CB 2.67 0.424:H:96:GLU:O 4:H:100:LYS:CB 2.67 0.422:E:120:SER:HA 2:E:121:ASN:HA 1.49 0.425:J:35:LYS:O 5:J:39:GLU:CB 2.67 0.428:P:4:LEU:O 8:P:8:LEU:CB 2.67 0.428:S:12:ALA:O 8:S:16:MET:CB 2.67 0.428:V:35:PHE:O 8:V:39:ALA:CB 2.67 0.42
2:D:10:GLY:HA2 2:D:59:SER:H 1.85 0.426:K:104:LEU:O 6:K:108:ILE:CB 2.68 0.427:L:59:SER:O 7:L:63:VAL:CB 2.68 0.421:A:208:VAL:O 1:A:212:LEU:CB 2.68 0.421:B:469:ALA:O 1:B:473:ALA:CB 2.67 0.421:C:464:ILE:O 1:C:468:GLU:CB 2.67 0.426:K:146:ASP:O 6:K:150:THR:CB 2.67 0.422:F:246:ARG:O 2:F:250:ALA:CB 2.67 0.421:B:505:ASP:O 1:B:509:ALA:HB3 2.19 0.422:F:363:ILE:O 2:F:367:TYR:CB 2.67 0.425:I:17:PHE:O 5:I:21:ALA:HB3 2.20 0.426:K:107:THR:O 6:K:111:TRP:CB 2.68 0.428:O:4:LEU:O 8:O:8:LEU:CB 2.68 0.428:S:35:PHE:O 8:S:39:ALA:CB 2.68 0.423:G:151:PRO:O 3:G:155:MET:CB 2.67 0.428:Q:12:ALA:O 8:Q:16:MET:CB 2.68 0.428:T:35:PHE:O 8:T:39:ALA:CB 2.67 0.425:I:13:ALA:O 5:I:17:PHE:CB 2.68 0.426:K:197:GLY:O 6:K:201:LEU:CB 2.67 0.428:N:35:PHE:O 8:N:39:ALA:CB 2.68 0.42
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:B:399:GLN:O 1:B:403:LEU:CB 2.68 0.421:B:422:ASP:O 1:B:426:LYS:CB 2.68 0.422:D:277:VAL:O 2:D:281:ARG:CB 2.68 0.423:G:233:GLU:O 3:G:237:SER:CB 2.68 0.427:L:31:LEU:O 7:L:35:ALA:CB 2.68 0.427:L:94:GLN:O 7:L:98:LEU:CB 2.68 0.428:M:4:LEU:O 8:M:8:LEU:CB 2.68 0.422:F:306:PRO:O 2:F:310:THR:CB 2.68 0.425:I:21:ALA:O 5:I:25:VAL:CB 2.68 0.425:J:125:ALA:O 5:J:129:VAL:CB 2.68 0.427:L:32:ALA:O 7:L:36:GLU:CB 2.67 0.428:T:35:PHE:O 8:T:39:ALA:HB3 2.20 0.421:A:500:LEU:O 1:A:504:LEU:CB 2.68 0.416:K:181:GLN:O 6:K:185:HIS:CB 2.67 0.417:L:126:ALA:O 7:L:130:LYS:CB 2.68 0.417:L:153:ARG:O 7:L:157:MET:CB 2.68 0.411:B:398:ALA:O 1:B:402:GLU:CB 2.68 0.411:C:500:LEU:O 1:C:504:LEU:CB 2.68 0.411:A:204:THR:O 1:A:208:VAL:CB 2.68 0.411:C:209:VAL:O 1:C:213:GLU:CB 2.69 0.412:F:385:GLU:O 2:F:389:VAL:CB 2.69 0.411:C:343:THR:O 1:C:347:SER:CB 2.68 0.412:E:157:VAL:O 2:E:161:GLU:CB 2.68 0.412:E:185:GLU:O 2:E:189:PHE:CB 2.68 0.412:F:275:MET:O 2:F:279:GLN:CB 2.68 0.412:F:149:GLY:HA3 2:F:321:LEU:H 1.84 0.418:R:35:PHE:O 8:R:39:ALA:CB 2.69 0.411:B:504:LEU:O 1:B:508:LYS:CB 2.69 0.411:A:209:VAL:O 1:A:213:GLU:CB 2.69 0.411:B:343:THR:O 1:B:347:SER:CB 2.69 0.412:D:404:PHE:H 2:D:407:ALA:HB3 1.86 0.413:G:103:LYS:O 3:G:107:ASP:CB 2.69 0.415:J:46:SER:O 5:J:50:ALA:CB 2.69 0.418:T:4:LEU:O 8:T:8:LEU:CB 2.68 0.411:A:496:ILE:O 1:A:500:LEU:CB 2.68 0.411:B:11:LEU:O 1:B:15:ARG:CB 2.68 0.411:C:444:GLN:O 1:C:448:LEU:CB 2.68 0.412:D:132:VAL:O 2:D:136:MET:CB 2.68 0.417:L:148:ALA:O 7:L:152:ILE:CB 2.68 0.418:Q:4:LEU:O 8:Q:8:LEU:CB 2.69 0.418:R:4:LEU:O 8:R:8:LEU:CB 2.69 0.41
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
2:F:-3:HIS:HA 2:F:71:LEU:HA 2.02 0.416:K:51:VAL:O 6:K:55:LEU:CB 2.69 0.412:E:393:ALA:O 2:E:397:GLN:CB 2.68 0.412:F:157:VAL:O 2:F:161:GLU:CB 2.69 0.413:G:74:ARG:HA 3:G:111:GLN:H 1.85 0.418:M:35:PHE:O 8:M:39:ALA:HB3 2.20 0.418:V:35:PHE:O 8:V:39:ALA:HB3 2.20 0.411:A:185:ASN:O 1:A:189:SER:CB 2.68 0.411:C:8:ILE:O 1:C:10:GLU:N 2.54 0.41
2:D:192:GLU:O 2:D:196:SER:CB 2.69 0.412:F:274:GLU:O 2:F:278:LEU:CB 2.69 0.417:L:95:PHE:O 7:L:99:ARG:CB 2.69 0.411:A:31:ILE:HA 1:A:41:ILE:HA 2.03 0.401:C:503:ILE:O 1:C:507:PHE:CB 2.68 0.402:D:223:GLY:O 2:D:227:ALA:HB3 2.21 0.402:E:220:ALA:O 2:E:224:LEU:CB 2.69 0.402:F:251:GLY:O 2:F:255:SER:CB 2.69 0.404:H:97:ALA:O 4:H:101:ALA:CB 2.69 0.402:E:385:GLU:O 2:E:389:VAL:CB 2.69 0.402:F:223:GLY:O 2:F:227:ALA:CB 2.69 0.403:G:212:LYS:O 3:G:216:ASP:CB 2.69 0.406:K:150:THR:O 6:K:154:ALA:CB 2.70 0.408:T:23:GLY:HA3 8:U:22:ILE:HA 2.04 0.401:A:205:ILE:O 1:A:209:VAL:CB 2.69 0.401:A:463:LYS:O 1:A:467:PHE:CB 2.69 0.401:A:470:ALA:O 1:A:474:TYR:CB 2.69 0.401:A:484:GLN:O 1:A:488:GLN:CB 2.69 0.401:B:500:LEU:O 1:B:504:LEU:CB 2.69 0.402:E:158:ASN:O 2:E:162:LEU:CB 2.69 0.405:I:12:ILE:O 5:I:16:LEU:CB 2.69 0.40
6:K:112:VAL:O 6:K:116:ASN:CB 2.70 0.408:T:12:ALA:O 8:T:16:MET:CB 2.69 0.401:A:483:MET:O 1:A:487:ASN:CB 2.69 0.401:B:443:GLN:O 1:B:447:VAL:CB 2.70 0.401:C:505:ASP:O 1:C:509:ALA:HB2 2.21 0.402:F:158:ASN:O 2:F:162:LEU:CB 2.69 0.404:H:119:ALA:O 4:H:123:LYS:CB 2.70 0.406:K:108:ILE:O 6:K:112:VAL:CB 2.69 0.408:U:35:PHE:O 8:U:39:ALA:CB 2.70 0.401:C:443:GLN:O 1:C:447:VAL:CB 2.70 0.402:E:214:GLY:O 2:E:218:ARG:CB 2.69 0.40
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
2:F:120:SER:H 2:F:285:THR:HA 1.86 0.402:F:309:ALA:O 2:F:313:ALA:CB 2.69 0.403:G:92:ILE:O 3:G:96:LYS:CB 2.69 0.408:R:12:ALA:O 8:R:16:MET:CB 2.69 0.40
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 509/513 (99%) 395 (78%) 98 (19%) 16 (3%) 4 35
1 B 508/513 (99%) 396 (78%) 94 (18%) 18 (4%) 4 32
1 C 506/513 (99%) 392 (78%) 93 (18%) 21 (4%) 3 28
2 D 464/471 (98%) 365 (79%) 73 (16%) 26 (6%) 2 24
2 E 464/471 (98%) 358 (77%) 90 (19%) 16 (3%) 4 33
2 F 464/471 (98%) 367 (79%) 77 (17%) 20 (4%) 3 28
3 G 282/287 (98%) 240 (85%) 34 (12%) 8 (3%) 5 37
4 H 134/139 (96%) 108 (81%) 21 (16%) 5 (4%) 4 31
5 I 153/155 (99%) 147 (96%) 6 (4%) 0 100 100
5 J 153/155 (99%) 146 (95%) 7 (5%) 0 100 100
6 K 207/271 (76%) 175 (84%) 22 (11%) 10 (5%) 2 26
7 L 158/177 (89%) 130 (82%) 26 (16%) 2 (1%) 13 54
8 M 73/79 (92%) 66 (90%) 5 (7%) 2 (3%) 5 38
8 N 73/79 (92%) 66 (90%) 4 (6%) 3 (4%) 3 29
8 O 73/79 (92%) 66 (90%) 4 (6%) 3 (4%) 3 29
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Mol Chain Analysed Favoured Allowed Outliers Percentiles
8 Q 73/79 (92%) 65 (89%) 6 (8%) 2 (3%) 5 38
8 R 73/79 (92%) 66 (90%) 4 (6%) 3 (4%) 3 29
8 S 73/79 (92%) 66 (90%) 4 (6%) 3 (4%) 3 29
8 T 73/79 (92%) 66 (90%) 4 (6%) 3 (4%) 3 29
8 U 73/79 (92%) 66 (90%) 4 (6%) 3 (4%) 3 29
8 V 73/79 (92%) 66 (90%) 4 (6%) 3 (4%) 3 29
All All 4732/4926 (96%) 3877 (82%) 685 (14%) 170 (4%) 7 32
All (170) Ramachandran outliers are listed below:
Mol Chain Res Type1 A 55 LEU1 A 120 PRO1 A 281 PRO1 B 55 LEU1 B 279 ARG1 B 281 PRO1 B 287 PRO1 C 55 LEU1 C 279 ARG2 D 17 PHE2 D 77 VAL2 D 138 PRO2 D 332 PRO2 D 345 ASP2 D 346 PRO2 E 17 PHE2 E 23 PRO2 E 211 GLU2 E 262 PRO2 E 298 VAL2 E 305 ASP2 E 345 ASP2 F 17 PHE2 F 113 ALA2 F 262 PRO3 G 189 PRO3 G 209 PRO3 G 210 ASP4 H 35 TYR
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Mol Chain Res Type4 H 72 GLN6 K 102 ALA6 K 126 LEU6 K 143 PRO6 K 181 GLN6 K 230 PRO8 M 47 PRO8 M 63 ILE8 N 47 PRO8 N 63 ILE8 O 47 PRO8 O 63 ILE8 P 47 PRO8 P 63 ILE8 Q 47 PRO8 Q 63 ILE8 R 47 PRO8 R 63 ILE8 S 47 PRO8 S 63 ILE8 T 47 PRO8 T 63 ILE8 U 47 PRO8 U 63 ILE8 V 47 PRO8 V 63 ILE1 A 137 ILE1 A 438 PRO1 C 9 SER1 C 85 GLY1 C 120 PRO2 D 78 PRO2 D 90 VAL2 D 405 PHE2 E 93 GLU2 E 346 PRO2 E 349 VAL4 H 46 LYS7 L 4 ILE1 A 114 PRO1 A 319 GLY1 B 5 SER
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Mol Chain Res Type1 B 85 GLY1 B 327 LEU1 B 454 GLY1 C 191 ILE1 C 414 ASP1 C 481 PRO2 D 0 MET2 D 74 PRO2 E 65 GLY2 F 79 VAL2 F 93 GLU2 F 117 GLU2 F 212 PRO2 F 414 PRO2 F 439 PRO3 G 4 LYS3 G 42 ARG3 G 162 GLY4 H 89 LEU6 K 142 VAL8 O 46 ILE1 A 69 ASP1 A 149 GLY1 A 310 GLU1 A 311 ALA1 B 88 VAL1 B 178 LEU1 C 114 PRO1 C 174 GLY1 C 178 LEU1 C 287 PRO2 D 18 PRO2 D 65 GLY2 D 93 GLU2 D 439 PRO2 E 336 PRO2 E 429 GLY2 E 436 ASP2 F 6 VAL2 F 94 PRO2 F 349 VAL3 G 208 GLU
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Mol Chain Res Type6 K 98 SER6 K 229 LEU1 A 216 GLY1 A 287 PRO1 B 22 VAL1 B 120 PRO1 B 134 PRO1 B 280 PRO1 C 280 PRO1 C 281 PRO2 D 305 ASP2 D 349 VAL2 F 23 PRO2 F 78 PRO2 F 85 GLY2 F 213 PRO2 F 345 ASP3 G 109 GLY8 P 46 ILE1 A 129 VAL1 B 148 THR1 C 370 PRO2 D -4 HIS2 D 33 ASN2 E 306 PRO2 E 433 GLY1 B 149 GLY1 C 113 ALA2 D 331 TYR6 K 121 LEU1 A 136 VAL1 C 282 GLY2 D 262 PRO2 F 433 GLY4 H 36 PRO1 B 198 ILE1 C 377 VAL1 C 454 GLY2 D 113 ALA2 D 175 VAL2 D 212 PRO6 K 101 ILE
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Mol Chain Res Type7 L 124 ILE8 T 43 PRO8 U 43 PRO1 A 32 VAL1 C 337 VAL8 N 43 PRO8 S 43 PRO1 B 282 GLY1 C 115 ILE2 D 92 GLY2 D 153 VAL2 F 8 VAL2 F 114 PRO8 R 43 PRO8 V 43 PRO
5.3.2 Protein sidechains iO
There are no protein residues with a non-rotameric sidechain to report in this entry.
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 carbohydrates in this entry.
5.6 Ligand geometry iO
4 ligands are modelled in this entry.
In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are de�ned in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bond
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length (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 LinkBond lengths Bond angles
Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2
9 ATP A 601 - 27,33,33 1.00 1 (3%) 27,52,52 1.85 4 (14%)
9 ATP B 601 - 27,33,33 1.00 1 (3%) 27,52,52 1.84 4 (14%)
9 ATP C 601 - 27,33,33 1.00 1 (3%) 27,52,52 1.84 4 (14%)
10 ADP D 601 - 25,29,29 1.03 1 (4%) 25,45,45 1.71 3 (12%)
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 de�ned in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.'-' means no outliers of that kind were identi�ed.
Mol Type Chain Res Link Chirals Torsions Rings9 ATP A 601 - - 0/18/38/38 0/3/3/39 ATP B 601 - - 0/18/38/38 0/3/3/39 ATP C 601 - - 0/18/38/38 0/3/3/310 ADP D 601 - - 0/12/32/32 0/3/3/3
All (4) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)10 D 601 ADP C5-C4 3.11 1.47 1.409 C 601 ATP C5-C4 3.13 1.47 1.409 B 601 ATP C5-C4 3.14 1.47 1.409 A 601 ATP C5-C4 3.14 1.47 1.40
All (15) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)9 A 601 ATP N3-C2-N1 -6.04 123.69 128.869 B 601 ATP N3-C2-N1 -6.00 123.73 128.869 C 601 ATP N3-C2-N1 -5.99 123.74 128.8610 D 601 ADP N3-C2-N1 -5.95 123.77 128.869 C 601 ATP PA-O3A-PB -3.61 120.50 132.639 A 601 ATP PA-O3A-PB -3.61 120.50 132.639 B 601 ATP PA-O3A-PB -3.59 120.56 132.639 A 601 ATP PB-O3B-PG -3.51 120.84 132.639 C 601 ATP PB-O3B-PG -3.50 120.87 132.639 B 601 ATP PB-O3B-PG -3.49 120.88 132.63
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Mol Chain Res Type Atoms Z Observed(o) Ideal(o)10 D 601 ADP PA-O3A-PB -3.24 121.74 132.6310 D 601 ADP C4-C5-N7 -2.94 106.57 109.419 C 601 ATP C4-C5-N7 -2.93 106.58 109.419 B 601 ATP C4-C5-N7 -2.92 106.59 109.419 A 601 ATP C4-C5-N7 -2.89 106.62 109.41
There are no chirality outliers.
There are no torsion outliers.
There are no ring outliers.
No monomer is involved in short contacts.
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.