Full wwPDB EM Map/Model Validation Report iO
Aug 10, 2020 � 02:09 AM BST
PDB ID : 6XBDEMDB ID : EMD-22116
Title : Cryo-EM structure of MlaFEDB in nanodiscs with phospholipid substratesAuthors : Coudray, N.; Isom, G.L.; MacRae, M.R.; Saiduddin, M.; Ekiert, D.C.; Bhabha,
G.Deposited on : 2020-06-05Resolution : 3.05 Å(reported)
Based on initial models : 5UW2, 6CM1
This is a Full wwPDB EM Map/Model Validation Report for a publicly released PDB entry.
We welcome your comments at [email protected] user guide is available at
https://www.wwpdb.org/validation/2017/EMValidationReportHelpwith speci�c help available everywhere you see the iO symbol.
The following versions of software and data (see references iO) were used in the production of this report:
EMDB validation analysis : 0.0.0.dev33Mogul : 1.8.5 (274361), CSD as541be (2020)
MolProbity : 4.02b-467buster-report : 1.1.7 (2018)
Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Ideal geometry (proteins) : Engh & Huber (2001)
Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.13.1
Page 2 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
1 Overall quality at a glance iO
The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY
The reported resolution of this entry is 3.05 Å.
Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.
MetricWhole archive(#Entries)
EM structures(#Entries)
Clashscore 158937 4297Ramachandran outliers 154571 4023
Sidechain outliers 154315 3826
The table below summarises the geometric issues observed across the polymeric chains and their�t to the map. The red, orange, yellow and green segments on the bar indicate the fraction ofresidues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. Agrey segment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions <=5%The upper red bar (where present) indicates the fraction of residues that have poor �t to the EMmap (all atom inclusion < 40%). The numeric value is given above the bar.
Mol Chain Length Quality of chain
1 A 201
1 B 201
1 C 201
1 D 201
1 E 201
1 F 201
2 G 260
2 H 260Continued on next page...
Page 3 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Continued from previous page...
Mol Chain Length Quality of chain
3 I 269
3 J 269
4 K 97
4 L 97
5 M 164
5 N 164
Page 4 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
2 Entry composition iO
There are 6 unique types of molecules in this entry. The entry contains 17433 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 Phospholipid ABC transporter-binding protein mlaD.
Mol Chain Residues Atoms AltConf Trace
1 A 144Total C N O S1108 715 178 213 2
0 0
1 B 138Total C N O S1063 687 170 204 2
0 0
1 C 144Total C N O S1033 652 172 208 1
0 0
1 D 143Total C N O S1096 707 177 210 2
0 0
1 E 145Total C N O S1112 718 179 213 2
0 0
1 F 143Total C N O S1028 649 171 207 1
0 0
There are 108 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA -17 MET - expression tag UNP H4UPP8A -16 HIS - expression tag UNP H4UPP8A -15 HIS - expression tag UNP H4UPP8A -14 HIS - expression tag UNP H4UPP8A -13 HIS - expression tag UNP H4UPP8A -12 HIS - expression tag UNP H4UPP8A -11 HIS - expression tag UNP H4UPP8A -10 GLN - expression tag UNP H4UPP8A -9 HIS - expression tag UNP H4UPP8A -8 GLN - expression tag UNP H4UPP8A -7 HIS - expression tag UNP H4UPP8A -6 GLU - expression tag UNP H4UPP8A -5 ASN - expression tag UNP H4UPP8A -4 LEU - expression tag UNP H4UPP8A -3 TYR - expression tag UNP H4UPP8A -2 PHE - expression tag UNP H4UPP8A -1 GLN - expression tag UNP H4UPP8A 0 GLY - expression tag UNP H4UPP8
Continued on next page...
Page 5 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Continued from previous page...
Chain Residue Modelled Actual Comment ReferenceB -17 MET - expression tag UNP H4UPP8B -16 HIS - expression tag UNP H4UPP8B -15 HIS - expression tag UNP H4UPP8B -14 HIS - expression tag UNP H4UPP8B -13 HIS - expression tag UNP H4UPP8B -12 HIS - expression tag UNP H4UPP8B -11 HIS - expression tag UNP H4UPP8B -10 GLN - expression tag UNP H4UPP8B -9 HIS - expression tag UNP H4UPP8B -8 GLN - expression tag UNP H4UPP8B -7 HIS - expression tag UNP H4UPP8B -6 GLU - expression tag UNP H4UPP8B -5 ASN - expression tag UNP H4UPP8B -4 LEU - expression tag UNP H4UPP8B -3 TYR - expression tag UNP H4UPP8B -2 PHE - expression tag UNP H4UPP8B -1 GLN - expression tag UNP H4UPP8B 0 GLY - expression tag UNP H4UPP8C -17 MET - expression tag UNP H4UPP8C -16 HIS - expression tag UNP H4UPP8C -15 HIS - expression tag UNP H4UPP8C -14 HIS - expression tag UNP H4UPP8C -13 HIS - expression tag UNP H4UPP8C -12 HIS - expression tag UNP H4UPP8C -11 HIS - expression tag UNP H4UPP8C -10 GLN - expression tag UNP H4UPP8C -9 HIS - expression tag UNP H4UPP8C -8 GLN - expression tag UNP H4UPP8C -7 HIS - expression tag UNP H4UPP8C -6 GLU - expression tag UNP H4UPP8C -5 ASN - expression tag UNP H4UPP8C -4 LEU - expression tag UNP H4UPP8C -3 TYR - expression tag UNP H4UPP8C -2 PHE - expression tag UNP H4UPP8C -1 GLN - expression tag UNP H4UPP8C 0 GLY - expression tag UNP H4UPP8D -17 MET - expression tag UNP H4UPP8D -16 HIS - expression tag UNP H4UPP8D -15 HIS - expression tag UNP H4UPP8D -14 HIS - expression tag UNP H4UPP8D -13 HIS - expression tag UNP H4UPP8D -12 HIS - expression tag UNP H4UPP8
Continued on next page...
Page 6 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Continued from previous page...
Chain Residue Modelled Actual Comment ReferenceD -11 HIS - expression tag UNP H4UPP8D -10 GLN - expression tag UNP H4UPP8D -9 HIS - expression tag UNP H4UPP8D -8 GLN - expression tag UNP H4UPP8D -7 HIS - expression tag UNP H4UPP8D -6 GLU - expression tag UNP H4UPP8D -5 ASN - expression tag UNP H4UPP8D -4 LEU - expression tag UNP H4UPP8D -3 TYR - expression tag UNP H4UPP8D -2 PHE - expression tag UNP H4UPP8D -1 GLN - expression tag UNP H4UPP8D 0 GLY - expression tag UNP H4UPP8E -17 MET - expression tag UNP H4UPP8E -16 HIS - expression tag UNP H4UPP8E -15 HIS - expression tag UNP H4UPP8E -14 HIS - expression tag UNP H4UPP8E -13 HIS - expression tag UNP H4UPP8E -12 HIS - expression tag UNP H4UPP8E -11 HIS - expression tag UNP H4UPP8E -10 GLN - expression tag UNP H4UPP8E -9 HIS - expression tag UNP H4UPP8E -8 GLN - expression tag UNP H4UPP8E -7 HIS - expression tag UNP H4UPP8E -6 GLU - expression tag UNP H4UPP8E -5 ASN - expression tag UNP H4UPP8E -4 LEU - expression tag UNP H4UPP8E -3 TYR - expression tag UNP H4UPP8E -2 PHE - expression tag UNP H4UPP8E -1 GLN - expression tag UNP H4UPP8E 0 GLY - expression tag UNP H4UPP8F -17 MET - expression tag UNP H4UPP8F -16 HIS - expression tag UNP H4UPP8F -15 HIS - expression tag UNP H4UPP8F -14 HIS - expression tag UNP H4UPP8F -13 HIS - expression tag UNP H4UPP8F -12 HIS - expression tag UNP H4UPP8F -11 HIS - expression tag UNP H4UPP8F -10 GLN - expression tag UNP H4UPP8F -9 HIS - expression tag UNP H4UPP8F -8 GLN - expression tag UNP H4UPP8F -7 HIS - expression tag UNP H4UPP8F -6 GLU - expression tag UNP H4UPP8
Continued on next page...
Page 7 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Continued from previous page...
Chain Residue Modelled Actual Comment ReferenceF -5 ASN - expression tag UNP H4UPP8F -4 LEU - expression tag UNP H4UPP8F -3 TYR - expression tag UNP H4UPP8F -2 PHE - expression tag UNP H4UPP8F -1 GLN - expression tag UNP H4UPP8F 0 GLY - expression tag UNP H4UPP8
� Molecule 2 is a protein called Phospholipid ABC transporter permease protein mlaE.
Mol Chain Residues Atoms AltConf Trace
2 G 256Total C N O S1926 1261 323 330 12
0 0
2 H 255Total C N O S1918 1257 321 328 12
0 0
� Molecule 3 is a protein called Phospholipid transport system ATP-binding protein MlaF.
Mol Chain Residues Atoms AltConf Trace
3 I 263Total C N O S1996 1268 352 362 14
0 0
3 J 263Total C N O S1996 1268 352 362 14
0 0
� Molecule 4 is a protein called Phospholipid ABC transporter-binding protein mlaB.
Mol Chain Residues Atoms AltConf Trace
4 K 95Total C N O S734 464 124 143 3
0 0
4 L 95Total C N O S734 464 124 143 3
0 0
� Molecule 5 is a protein called MSP1D1.
Mol Chain Residues Atoms AltConf Trace
5 M 164Total C N O821 492 164 165
0 0
5 N 156Total C N O780 468 156 156
0 0
� Molecule 6 is DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE (three-lettercode: PEF) (formula: C37H74NO8P) (labeled as "Ligand of Interest" by author).
Page 8 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Mol Chain Residues Atoms AltConf
6 G 1Total C O P88 70 16 2
0
6 G 1Total C O P88 70 16 2
0
Page 9 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
3 Residue-property plots iO
These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The�rst graphic for a chain summarises the proportions of the various outlier classes displayed in thesecond graphic. The second graphic shows the sequence view annotated by issues in geometry andatom inclusion in map density. Residues are color-coded according to the number of geometricquality criteria for which they contain at least one outlier: green = 0, yellow = 1, orange = 2and red = 3 or more. A red diamond above a residue indicates a poor �t to the EM map forthis residue (all atom inclusion < 40%). Stretches of 2 or more consecutive residues without anyoutlier are shown as a green connector. Residues present in the sample, but not in the model, areshown in grey.
• Molecule 1: Phospholipid ABC transporter-binding protein mlaD
Chain A:
MET
HIS
HIS
HIS
HIS
HIS
HIS
GLN
HIS
GLN
HIS
GLU
ASN
LEU
TYR
PHE
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MET
Q2
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K27
A28
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T36
Y40
T41
L42
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D47
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I49
R55
I60
V65
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ASN
GLU
THR
THR
GLU
PRO
VAL
GLY
THR
THR
LYS
• Molecule 1: Phospholipid ABC transporter-binding protein mlaD
Chain B:
MET
HIS
HIS
HIS
HIS
HIS
HIS
GLN
HIS
GLN
HIS
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ASN
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A54
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PRO
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GLY
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LYS
• Molecule 1: Phospholipid ABC transporter-binding protein mlaD
Chain C:
MET
HIS
HIS
HIS
HIS
HIS
HIS
GLN
HIS
GLN
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ASN
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PRO
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GLY
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• Molecule 1: Phospholipid ABC transporter-binding protein mlaD
Page 10 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Chain D:
MET
HIS
HIS
HIS
HIS
HIS
HIS
GLN
HIS
GLN
HIS
GLU
ASN
LEU
TYR
PHE
GLN
GLY
MET
Q2
K5
K27
A28
A29
ASN
VAL
THR
SER
ILE
ARG
T36
E37
I49
A69
D70
I71
T72
L73
T83
R102
P121
GLU
LEU
G124
D132
T133
V142
Y152
GLY
SER
LYS
GLY
ASP
ASP
ASN
LYS
ASN
SER
GLY
ASP
ALA
PRO
ALA
ALA
ALA
PRO
GLY
ASN
ASN
GLU
THR
THR
GLU
PRO
VAL
GLY
THR
THR
LYS
• Molecule 1: Phospholipid ABC transporter-binding protein mlaD
Chain E:
MET
HIS
HIS
HIS
HIS
HIS
HIS
GLN
HIS
GLN
HIS
GLU
ASN
LEU
TYR
PHE
GLN
GLY
MET
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K4
I8
I12
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SER
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ARG
T36
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PRO
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GLY
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LYS
• Molecule 1: Phospholipid ABC transporter-binding protein mlaD
Chain F:
MET
HIS
HIS
HIS
HIS
HIS
HIS
GLN
HIS
GLN
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GLU
ASN
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• Molecule 2: Phospholipid ABC transporter permease protein mlaE
Chain G:
MET
LEU
LEU
N4
R18
R22
L25
K34
�P35
E36
F37
R38
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I58
I66
L70
Q73
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L90
L93
S94
E98
L99
G100
V103
G113
S114
E119
T126
R141
R147
L155
F162
W168
L172
M189
Q190
N191
A192
V193
D194
W195
R196
M197
D198
A210
S217
D223
S232
T235
V240
L244
T254
G259
ASN
• Molecule 2: Phospholipid ABC transporter permease protein mlaE
Chain H:
MET
LEU
LEU
ASN
A5
G10
K34
�P35
E36
F37
R38
K39
H40
Y49
S55
I58
L70
Y75
S82
L90
L93
E98
L99
G100
F108
G113
S114
A118
E119
M135
P139
L140
R141
R142
V143
I144
S145
P146
R147
F148
W149
L155
Page 11 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
F162
W168
L172
W177
V193
D194
K205
A210
I225
P226
T227
G230
T235
V240
L256
M257
F258
G259
ASN
• Molecule 3: Phospholipid transport system ATP-binding protein MlaF
Chain I:
MET
GLU
GLN
SER
V5
D13
C22
S28
I39
M40
I45
T49
L50
L51
R52
L53
I58
F67
I72
M87
A95
M100
N101
D104
N105
V106
K128
L129
E130
A131
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G136
A137
L140
S146
G147
R151
R157
A160
L165
I166
M167
E170
P171
G181
V184
V201
S202
H203
L209
L218
K221
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R241
Q242
V252
R255
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L266
P267
GLY
SER
• Molecule 3: Phospholipid transport system ATP-binding protein MlaF
Chain J:
MET
GLU
GLN
SER
V5
�
D13
C22
S28
I39
M40
I45
T49
L50
L51
R52
L53
I58
F67
I72
K85
R86
M87
Q92
A95
M100
D104
N105
V106
H113
K128
L129
E130
A131
R135
G136
A137
L140
S146
G147
R151
R157
A160
L165
I166
M167
E170
P171
G181
V184
V201
S202
H203
L209
L218
K221
L232
R241
Q242
V252
R255
D260
P267
GLY
SER
• Molecule 4: Phospholipid ABC transporter-binding protein mlaB
Chain K:
MET
SER
E3
S6
W7
L14
S17
D21
Q22
D23
V24
L25
L26
E30
I39
L44
D51
L55
L59
I62
K66
N70
L74
V77
K80
V81
Y82
A85
Y88
N89
L90
D93
V94
L95
P96
R97
• Molecule 4: Phospholipid ABC transporter-binding protein mlaB
Chain L:
MET
SER
E3
S6
W7
L14
S17
D21
Q22
D23
V24
L25
L26
E30
I39
L44
D51
L55
L59
I62
D63
K66
N70
L74
V77
K80
V81
A85
Y88
N89
L90
D93
V94
L95
P96
R97
• Molecule 5: MSP1D1
Chain M:
X1
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Page 12 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
• Molecule 5: MSP1D1
Chain N:
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Page 13 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
4 Experimental information iO
Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C1 DepositorNumber of particles used 731205 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) 71 Depositor
Minimum defocus (nm) Not provided DepositorMaximum defocus (nm) Not provided DepositorMagni�cation 29000 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 1.904 DepositorMinimum map value -0.909 DepositorAverage map value 0.001 DepositorMap value standard deviation 0.071 DepositorRecommended contour level 0.27 DepositorMap size (Å) 249.6, 249.6, 249.6 DepositorMap dimensions 300, 300, 300 DepositorMap angles (◦) 90.0, 90.0, 90.0 DepositorPixel spacing (Å) 0.832, 0.832, 0.832 Depositor
Page 14 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
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:PEF
The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
Mol ChainBond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5
1 A 0.25 0/1126 0.47 0/15311 B 0.25 0/1081 0.43 0/14701 C 0.25 0/1047 0.47 0/14291 D 0.25 0/1113 0.43 0/15121 E 0.25 0/1130 0.45 0/15371 F 0.25 0/1042 0.47 0/14222 G 0.26 0/1964 0.45 0/26692 H 0.26 0/1956 0.44 0/26583 I 0.25 0/2036 0.43 0/27643 J 0.25 0/2036 0.43 0/27644 K 0.26 0/743 0.44 0/10084 L 0.26 0/743 0.44 0/1008All All 0.25 0/16017 0.44 0/21772
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 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 1108 0 1133 22 0
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Page 15 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
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Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 B 1063 0 1082 21 01 C 1033 0 973 14 01 D 1096 0 1120 11 01 E 1112 0 1138 16 01 F 1028 0 971 21 02 G 1926 0 2029 46 02 H 1918 0 2023 37 03 I 1996 0 2039 30 03 J 1996 0 2039 32 04 K 734 0 755 20 04 L 734 0 755 21 05 M 821 0 166 22 05 N 780 0 158 29 06 G 88 0 134 9 0All All 17433 0 16515 298 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 9.
All (298) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:F:53:LYS:CD 2:G:191:ASN:HD22 1.61 1.131:F:53:LYS:HD3 2:G:191:ASN:ND2 1.68 1.071:F:53:LYS:CD 2:G:191:ASN:ND2 2.30 0.911:F:53:LYS:CG 2:G:191:ASN:HD22 1.84 0.892:G:89:MET:HG3 2:G:193:VAL:HG21 1.53 0.872:H:93:LEU:HD21 2:H:193:VAL:HB 1.55 0.851:F:53:LYS:CG 2:G:191:ASN:ND2 2.44 0.801:A:55:ARG:HD3 2:G:195:TRP:HZ3 1.49 0.762:H:93:LEU:HD11 2:H:193:VAL:CG1 2.16 0.761:A:55:ARG:HE 2:G:195:TRP:HE3 1.31 0.761:A:43:TYR:HB2 1:A:133:THR:HG22 1.68 0.752:H:93:LEU:HD11 2:H:193:VAL:HG11 1.73 0.711:D:142:VAL:HG21 1:E:102:ARG:HD3 1.72 0.714:K:44:LEU:HD12 4:K:77:VAL:HG22 1.74 0.701:E:69:ALA:HB3 1:E:83:THR:HG23 1.75 0.695:N:77:UNK:O 5:N:81:UNK:N 2.24 0.69
1:A:55:ARG:HD3 2:G:195:TRP:CZ3 2.27 0.692:G:126:THR:O 2:G:126:THR:HG22 1.93 0.694:L:44:LEU:HD12 4:L:77:VAL:HG22 1.74 0.69
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Page 16 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:C:69:ALA:HB3 1:C:83:THR:HG23 1.76 0.685:M:66:UNK:O 5:M:70:UNK:N 2.27 0.684:L:6:SER:HG 4:L:17:SER:HG 1.43 0.66
2:G:58:ILE:HD12 2:H:240:VAL:HG13 1.77 0.664:K:6:SER:HG 4:K:17:SER:HG 1.41 0.661:F:53:LYS:HG2 2:G:191:ASN:HD22 1.58 0.65
2:G:240:VAL:HG13 2:H:58:ILE:HD12 1.78 0.652:H:114:SER:HB2 2:H:235:THR:HG23 1.77 0.652:G:70:LEU:HD11 2:G:99:LEU:HD12 1.79 0.641:F:53:LYS:HG2 2:G:191:ASN:ND2 2.13 0.645:N:73:UNK:O 5:N:77:UNK:N 2.30 0.641:B:88:GLN:NE2 1:B:91:ASN:OD1 2.31 0.642:G:22:ARG:NH1 2:G:223:ASP:OD2 2.31 0.642:G:114:SER:HB2 2:G:235:THR:HG23 1.79 0.632:H:70:LEU:HD11 2:H:99:LEU:HD12 1.78 0.633:J:22:CYS:HB3 3:J:221:LYS:HE3 1.80 0.635:N:130:UNK:O 5:N:134:UNK:N 2.32 0.635:M:74:UNK:O 5:M:78:UNK:N 2.33 0.625:M:99:UNK:O 5:M:103:UNK:N 2.33 0.621:F:37:GLU:OE2 1:F:89:ARG:NH1 2.33 0.623:I:22:CYS:HB3 3:I:221:LYS:HE3 1.80 0.621:F:129:LYS:N 1:F:132:ASP:OD2 2.31 0.625:N:62:UNK:O 5:N:66:UNK:N 2.33 0.625:N:84:UNK:O 5:N:88:UNK:N 2.33 0.614:K:85:ALA:HB1 4:K:90:LEU:HD12 1.82 0.615:N:30:UNK:O 5:N:34:UNK:N 2.33 0.61
2:G:232:SER:HB3 2:H:118:ALA:HB1 1.81 0.614:L:85:ALA:HB1 4:L:90:LEU:HD12 1.82 0.615:M:59:UNK:O 5:M:63:UNK:N 2.34 0.611:B:49:ILE:HD13 1:B:71:ILE:HG21 1.83 0.601:B:103:THR:HG22 1:B:110:GLN:HG2 1.82 0.605:N:81:UNK:O 5:N:85:UNK:N 2.34 0.60
2:H:227:THR:HG23 2:H:230:GLY:H 1.66 0.595:M:63:UNK:O 5:M:67:UNK:N 2.34 0.592:G:36:GLU:HA 2:G:141:ARG:HH12 1.67 0.595:M:77:UNK:O 5:M:81:UNK:N 2.34 0.591:A:71:ILE:HG12 1:A:82:VAL:HG12 1.85 0.584:L:7:TRP:HB2 4:L:14:LEU:HD11 1.85 0.585:M:69:UNK:O 5:M:73:UNK:N 2.36 0.581:B:53:LYS:NZ 2:H:75:TYR:OH 2.37 0.582:G:73:GLN:NE2 2:H:98:GLU:OE1 2.37 0.58
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Page 17 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
4:K:39:ILE:O 4:K:70:ASN:ND2 2.37 0.585:N:45:UNK:O 5:N:49:UNK:N 2.36 0.584:K:7:TRP:HB2 4:K:14:LEU:HD11 1.85 0.584:L:39:ILE:O 4:L:70:ASN:ND2 2.37 0.58
5:M:134:UNK:O 5:M:138:UNK:N 2.36 0.585:N:87:UNK:O 5:N:91:UNK:N 2.37 0.58
4:K:62:ILE:HD11 4:K:74:LEU:HD21 1.87 0.571:E:8:ILE:O 1:E:12:ILE:HG13 2.04 0.57
1:A:41:THR:HG22 1:A:85:GLU:HG2 1.86 0.571:E:49:ILE:HD13 1:E:71:ILE:HG21 1.87 0.575:N:86:UNK:O 5:N:90:UNK:N 2.38 0.574:L:62:ILE:HD11 4:L:74:LEU:HD21 1.87 0.575:N:70:UNK:O 5:N:74:UNK:N 2.38 0.561:D:69:ALA:HB3 1:D:83:THR:HG23 1.86 0.561:E:71:ILE:HG12 1:E:82:VAL:HG23 1.87 0.561:B:69:ALA:HB3 1:B:83:THR:HG23 1.87 0.562:G:89:MET:HG3 2:G:193:VAL:CG2 2.31 0.555:M:25:UNK:O 5:M:29:UNK:N 2.39 0.552:G:94:SER:HA 6:G:302:PEF:H351 1.87 0.555:M:62:UNK:O 5:M:66:UNK:N 2.39 0.55
1:B:10:VAL:HG11 2:G:25:LEU:HG 1.88 0.551:C:36:THR:OG1 1:C:37:GLU:N 2.40 0.555:N:105:UNK:O 5:N:109:UNK:N 2.40 0.552:H:93:LEU:CD1 2:H:193:VAL:HG11 2.36 0.551:B:55:ARG:NH2 2:H:177:TRP:O 2.40 0.553:I:232:LEU:O 3:I:241:ARG:NH2 2.38 0.55
1:D:49:ILE:HD13 1:D:71:ILE:HG21 1.89 0.552:G:155:LEU:HB3 2:G:210:ALA:HB2 1.89 0.552:H:155:LEU:HB3 2:H:210:ALA:HB2 1.89 0.553:J:95:ALA:O 3:J:157:ARG:NH1 2.40 0.54
3:J:51:LEU:HD22 3:J:167:MET:HB3 1.90 0.543:I:95:ALA:O 3:I:157:ARG:NH1 2.41 0.54
3:I:87:MET:HG2 3:I:165:LEU:HD23 1.89 0.544:L:66:LYS:NZ 4:L:93:ASP:O 2.41 0.541:A:55:ARG:NE 2:G:195:TRP:HE3 2.03 0.542:H:36:GLU:O 2:H:40:HIS:ND1 2.41 0.543:J:232:LEU:O 3:J:241:ARG:NH2 2.38 0.545:M:80:UNK:O 5:M:84:UNK:N 2.41 0.541:F:36:THR:OG1 1:F:37:GLU:N 2.41 0.541:E:103:THR:HG22 1:E:110:GLN:HG2 1.90 0.531:B:95:ASP:OD2 1:B:126:ALA:N 2.41 0.53
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Page 18 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:A:49:ILE:HD13 1:A:71:ILE:HG21 1.90 0.534:K:66:LYS:NZ 4:K:93:ASP:O 2.41 0.53
1:A:84:LEU:HD13 1:A:86:ILE:HG13 1.90 0.533:I:51:LEU:HD22 3:I:167:MET:HB3 1.90 0.535:N:97:UNK:O 5:N:101:UNK:N 2.42 0.53
3:I:151:ARG:NH2 3:I:171:PRO:O 2.41 0.533:J:87:MET:HG2 3:J:165:LEU:HD23 1.89 0.535:M:81:UNK:O 5:M:85:UNK:N 2.42 0.535:N:108:UNK:O 5:N:112:UNK:N 2.42 0.525:N:41:UNK:O 5:N:45:UNK:N 2.41 0.524:L:6:SER:OG 4:L:17:SER:OG 2.22 0.52
3:I:170:GLU:HG3 3:I:202:SER:HA 1.92 0.523:J:151:ARG:NH2 3:J:171:PRO:O 2.41 0.521:D:28:ALA:HA 2:H:194:ASP:CB 2.40 0.523:J:131:ALA:HB2 4:L:88:TYR:CD1 2.45 0.522:H:36:GLU:OE2 2:H:149:TRP:NE1 2.38 0.511:C:95:ASP:OD1 1:C:95:ASP:N 2.42 0.511:F:53:LYS:HB3 2:G:191:ASN:HD21 1.75 0.511:B:120:ASP:HB2 1:B:123:LEU:HB2 1.92 0.515:N:101:UNK:O 5:N:105:UNK:N 2.43 0.514:K:26:LEU:O 4:K:30:GLU:HG3 2.11 0.51
3:J:170:GLU:HG3 3:J:202:SER:HA 1.92 0.515:N:99:UNK:O 5:N:103:UNK:N 2.44 0.511:A:27:LYS:O 2:G:189:MET:HE3 2.11 0.51
1:E:29:ALA:HB2 2:H:256:LEU:HD23 1.92 0.515:M:5:UNK:O 5:M:9:UNK:N 2.44 0.51
1:C:52:LEU:HD21 1:C:68:VAL:HG21 1.93 0.511:E:38:PRO:HB2 1:E:88:GLN:H 1.76 0.501:F:53:LYS:CE 2:G:191:ASN:HD22 2.21 0.504:L:26:LEU:O 4:L:30:GLU:HG3 2.11 0.50
3:I:53:LEU:HD23 3:I:58:ILE:HG13 1.94 0.505:N:98:UNK:O 5:N:102:UNK:N 2.45 0.505:N:126:UNK:O 5:N:130:UNK:N 2.45 0.50
6:G:302:PEF:H221 2:H:90:LEU:HD11 1.93 0.503:I:131:ALA:HB2 4:K:88:TYR:CD1 2.46 0.501:F:101:ILE:HG12 1:F:112:LEU:HD23 1.93 0.494:K:23:ASP:OD1 4:K:24:VAL:HG13 2.12 0.491:B:132:ASP:OD1 1:B:133:THR:N 2.45 0.494:L:95:LEU:O 4:L:97:ARG:NH1 2.46 0.49
1:A:42:LEU:HB2 1:A:84:LEU:HD11 1.92 0.491:A:102:ARG:HG2 1:F:144:GLU:HG3 1.94 0.49
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
3:J:53:LEU:HD23 3:J:58:ILE:HG13 1.94 0.494:L:23:ASP:OD1 4:L:24:VAL:HG13 2.12 0.491:C:94:PRO:HG3 1:C:119:GLU:HG3 1.95 0.492:H:119:GLU:OE2 2:H:147:ARG:NH2 2.35 0.494:K:95:LEU:O 4:K:97:ARG:NH1 2.46 0.49
3:I:106:VAL:HG21 3:I:129:LEU:HD21 1.95 0.491:E:77:THR:HG23 1:E:79:LEU:H 1.78 0.481:F:49:ILE:HD13 1:F:71:ILE:HG21 1.93 0.483:I:40:MET:HE1 3:I:209:LEU:HD21 1.95 0.485:N:52:UNK:O 5:N:56:UNK:N 2.45 0.48
1:D:132:ASP:OD1 1:D:133:THR:N 2.45 0.485:N:95:UNK:O 5:N:99:UNK:N 2.46 0.48
1:A:60:ILE:HG13 1:A:65:VAL:HG21 1.95 0.481:E:37:GLU:HA 1:E:39:THR:HG23 1.95 0.483:I:128:LYS:HE3 3:I:160:ALA:HA 1.95 0.483:J:128:LYS:HE3 3:J:160:ALA:HA 1.95 0.481:B:49:ILE:HD12 1:B:71:ILE:HD13 1.96 0.481:D:73:LEU:HG 1:E:63:VAL:HG11 1.95 0.482:G:126:THR:O 2:G:126:THR:CG2 2.61 0.48
1:A:146:LEU:HD11 1:F:147:ILE:HD13 1.96 0.481:D:5:LYS:NZ 2:H:49:TYR:OH 2.47 0.471:B:38:PRO:O 1:B:88:GLN:HB2 2.14 0.475:N:42:UNK:O 5:N:46:UNK:N 2.47 0.47
3:J:106:VAL:HG21 3:J:129:LEU:HD21 1.95 0.473:I:130:GLU:OE2 3:J:255:ARG:NH2 2.48 0.473:J:146:SER:OG 3:J:147:GLY:N 2.48 0.474:L:55:LEU:O 4:L:59:LEU:HG 2.15 0.47
4:K:62:ILE:HD13 4:K:96:PRO:HD2 1.97 0.471:E:132:ASP:OD1 1:E:133:THR:N 2.44 0.472:G:100:GLY:HA2 2:G:162:PHE:CE2 2.50 0.475:M:60:UNK:O 5:M:64:UNK:N 2.48 0.47
6:G:302:PEF:H362 6:G:302:PEF:H332 1.73 0.461:C:144:GLU:HG3 1:D:102:ARG:HG2 1.98 0.462:H:100:GLY:HA2 2:H:162:PHE:CE2 2.51 0.463:I:242:GLN:HE22 3:I:252:VAL:HB 1.81 0.465:M:102:UNK:O 5:M:106:UNK:N 2.48 0.461:F:7:GLU:O 2:H:10:GLY:HA3 2.16 0.465:N:67:UNK:O 5:N:71:UNK:N 2.49 0.46
1:C:58:VAL:HG22 1:C:112:LEU:HB2 1.97 0.461:C:49:ILE:HD13 1:C:71:ILE:HG21 1.98 0.461:F:142:VAL:HG23 1:F:145:ASP:HB2 1.96 0.46
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
4:L:62:ILE:HD13 4:L:96:PRO:HD2 1.97 0.461:C:46:PHE:HZ 1:C:99:LEU:HD23 1.81 0.46
2:G:93:LEU:HD22 2:G:198:ASP:OD2 2.15 0.461:E:49:ILE:HD12 1:E:71:ILE:HD13 1.97 0.466:G:301:PEF:H201 6:G:301:PEF:H172 1.72 0.462:G:66:ILE:CD1 2:G:103:VAL:HG11 2.46 0.463:J:40:MET:HE1 3:J:209:LEU:HD21 1.98 0.461:C:130:ASP:OD1 1:C:131:GLY:N 2.48 0.462:G:90:LEU:HD12 6:G:302:PEF:H312 1.98 0.462:G:36:GLU:HG2 2:G:37:PHE:HD1 1.80 0.463:I:146:SER:OG 3:I:147:GLY:N 2.48 0.464:K:21:ASP:OD1 4:K:21:ASP:N 2.49 0.461:B:7:GLU:HA 1:B:10:VAL:HG12 1.96 0.45
2:G:119:GLU:OE2 2:G:147:ARG:NH2 2.34 0.454:K:55:LEU:O 4:K:59:LEU:HG 2.15 0.454:L:21:ASP:OD1 4:L:21:ASP:N 2.49 0.451:A:152:TYR:HE1 1:B:149:GLN:HE22 1.62 0.451:D:2:GLN:OE1 1:D:2:GLN:N 2.49 0.451:A:27:LYS:HB3 2:G:189:MET:CE 2.47 0.45
1:E:107:LEU:HD11 6:G:301:PEF:H212 1.99 0.451:B:7:GLU:OE2 2:G:18:ARG:HA 2.17 0.453:I:255:ARG:NH2 3:J:130:GLU:OE2 2.49 0.452:H:55:SER:O 2:H:55:SER:OG 2.33 0.455:N:91:UNK:O 5:N:95:UNK:N 2.49 0.45
3:J:242:GLN:HE22 3:J:252:VAL:HB 1.81 0.451:E:25:CYS:HB3 2:H:256:LEU:HD21 1.98 0.453:J:39:ILE:HB 3:J:201:VAL:HG22 1.99 0.451:A:47:ASP:N 1:A:47:ASP:OD1 2.49 0.451:B:119:GLU:N 1:B:119:GLU:OE1 2.46 0.451:C:129:LYS:N 1:C:132:ASP:OD2 2.50 0.45
1:B:39:THR:HG22 1:B:87:GLU:HA 1.99 0.445:M:128:UNK:O 5:M:132:UNK:N 2.50 0.443:I:39:ILE:HB 3:I:201:VAL:HG22 1.99 0.444:K:6:SER:OG 4:K:17:SER:OG 2.22 0.44
1:D:36:THR:OG1 1:D:37:GLU:N 2.51 0.443:I:202:SER:OG 3:I:203:HIS:N 2.51 0.443:I:135:ARG:NH1 3:J:260:ASP:O 2.49 0.444:L:80:LYS:HB2 4:L:80:LYS:HE3 1.79 0.445:M:133:UNK:O 5:M:137:UNK:N 2.51 0.443:J:202:SER:OG 3:J:203:HIS:N 2.51 0.432:H:108:PHE:O 2:H:113:GLY:N 2.51 0.43
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Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
2:H:225:ILE:HG22 2:H:227:THR:HG22 2.00 0.433:I:101:ASN:O 3:I:105:ASN:ND2 2.45 0.433:I:260:ASP:O 3:J:135:ARG:NH1 2.49 0.435:N:96:UNK:O 5:N:100:UNK:N 2.52 0.43
2:G:168:TRP:CH2 2:G:172:LEU:HD11 2.54 0.432:G:36:GLU:HA 2:G:141:ARG:NH1 2.33 0.436:G:302:PEF:H402 2:H:99:LEU:HD11 2.00 0.432:H:145:SER:OG 2:H:146:PRO:HD3 2.19 0.431:C:101:ILE:HG12 1:C:112:LEU:HD23 2.00 0.432:H:168:TRP:CH2 2:H:172:LEU:HD11 2.54 0.435:M:88:UNK:O 5:M:92:UNK:N 2.51 0.43
2:H:135:MET:HE1 3:J:157:ARG:HH21 1.83 0.433:I:181:GLY:HA2 3:I:184:VAL:HG12 2.01 0.435:M:2:UNK:O 5:M:6:UNK:N 2.52 0.434:K:21:ASP:HA 4:K:51:ASP:OD1 2.19 0.434:L:23:ASP:OD1 4:L:24:VAL:N 2.52 0.435:N:80:UNK:O 5:N:84:UNK:N 2.52 0.43
3:J:181:GLY:HA2 3:J:184:VAL:HG12 2.01 0.422:G:113:GLY:O 2:G:217:SER:HB2 2.19 0.425:M:142:UNK:O 5:M:146:UNK:N 2.52 0.421:A:88:GLN:HE21 1:A:91:ASN:ND2 2.17 0.421:D:27:LYS:HA 1:D:27:LYS:HD3 1.87 0.424:K:82:TYR:OH 4:K:97:ARG:O 2.29 0.424:L:21:ASP:HA 4:L:51:ASP:OD1 2.19 0.421:E:129:LYS:HB3 1:E:129:LYS:HE2 1.84 0.423:J:92:GLN:O 3:J:151:ARG:NE 2.48 0.42
4:L:55:LEU:HD21 4:L:81:VAL:HG13 2.02 0.424:K:23:ASP:OD1 4:K:24:VAL:N 2.52 0.421:F:38:PRO:O 1:F:88:GLN:HB2 2.18 0.42
2:H:36:GLU:HB2 2:H:141:ARG:HH12 1.84 0.422:G:36:GLU:HG2 2:G:37:PHE:CD1 2.54 0.425:M:127:UNK:O 5:M:131:UNK:N 2.53 0.425:N:33:UNK:O 5:N:37:UNK:N 2.53 0.42
6:G:302:PEF:H361 6:G:302:PEF:H392 1.58 0.423:I:39:ILE:HG21 3:I:50:LEU:HD23 2.02 0.425:N:78:UNK:O 5:N:82:UNK:N 2.53 0.423:J:13:ASP:H 3:J:28:SER:HB3 1.85 0.41
1:A:76:LYS:HD2 1:A:76:LYS:HA 1.86 0.411:B:142:VAL:HG23 1:B:145:ASP:HB2 2.03 0.413:J:131:ALA:HB2 4:L:88:TYR:HD1 1.85 0.411:A:88:GLN:HE21 1:A:91:ASN:HD21 1.67 0.41
Continued on next page...
Page 22 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Continued from previous page...
Atom-1 Atom-2Interatomicdistance (Å)
Clashoverlap (Å)
1:C:48:ASN:N 1:C:139:SER:OG 2.48 0.413:J:39:ILE:HG21 3:J:50:LEU:HD23 2.02 0.414:K:80:LYS:HE3 4:K:80:LYS:HB2 1.79 0.413:I:45:ILE:HD13 3:I:218:LEU:HD23 2.02 0.413:I:49:THR:HG23 3:I:58:ILE:HD11 2.03 0.413:I:67:PHE:HB2 3:I:72:ILE:HD11 2.02 0.412:H:139:PRO:O 2:H:143:VAL:HG12 2.20 0.413:I:100:MET:HB2 3:I:104:ASP:HB2 2.02 0.413:J:45:ILE:HD13 3:J:218:LEU:HD23 2.02 0.415:N:1:UNK:O 5:N:5:UNK:N 2.53 0.41
1:A:40:TYR:CE2 1:A:42:LEU:HD11 2.55 0.413:I:13:ASP:H 3:I:28:SER:HB3 1.85 0.41
3:J:137:ALA:HA 3:J:140:LEU:HD13 2.02 0.411:F:53:LYS:CB 2:G:191:ASN:ND2 2.84 0.412:H:38:ARG:HA 2:H:38:ARG:HD3 1.82 0.413:J:49:THR:HG23 3:J:58:ILE:HD11 2.03 0.414:K:55:LEU:HD21 4:K:81:VAL:HG13 2.02 0.412:G:81:TYR:OH 6:G:301:PEF:H121 2.21 0.412:G:98:GLU:OE2 2:G:254:THR:OG1 2.38 0.413:J:67:PHE:HB2 3:J:72:ILE:HD11 2.02 0.41
1:A:106:LEU:HD23 1:F:106:LEU:HD22 2.03 0.401:B:112:LEU:HD23 1:B:112:LEU:HA 1.91 0.401:B:95:ASP:HA 1:B:128:LEU:HD21 2.03 0.401:B:107:LEU:O 2:H:82:SER:HB3 2.21 0.405:M:156:UNK:O 5:M:160:UNK:N 2.54 0.40
1:C:142:VAL:HG23 1:C:145:ASP:OD1 2.22 0.402:G:99:LEU:HD23 2:G:99:LEU:HA 1.87 0.402:H:205:LYS:HE3 2:H:257:MET:HE1 2.02 0.403:J:100:MET:HB2 3:J:104:ASP:HB2 2.02 0.402:G:244:LEU:HD21 2:H:58:ILE:HG13 2.03 0.403:I:137:ALA:HA 3:I:140:LEU:HD13 2.02 0.403:J:85:LYS:HE2 3:J:113:HIS:ND1 2.37 0.40
3:I:266:LEU:HD13 4:L:63:ASP:HB2 2.04 0.40
There are no symmetry-related clashes.
Page 23 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
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 140/201 (70%) 136 (97%) 4 (3%) 0 100 100
1 B 134/201 (67%) 129 (96%) 5 (4%) 0 100 100
1 C 140/201 (70%) 137 (98%) 3 (2%) 0 100 100
1 D 137/201 (68%) 134 (98%) 3 (2%) 0 100 100
1 E 141/201 (70%) 131 (93%) 10 (7%) 0 100 100
1 F 139/201 (69%) 132 (95%) 7 (5%) 0 100 100
2 G 254/260 (98%) 248 (98%) 6 (2%) 0 100 100
2 H 253/260 (97%) 242 (96%) 11 (4%) 0 100 100
3 I 261/269 (97%) 253 (97%) 8 (3%) 0 100 100
3 J 261/269 (97%) 253 (97%) 8 (3%) 0 100 100
4 K 93/97 (96%) 90 (97%) 3 (3%) 0 100 100
4 L 93/97 (96%) 90 (97%) 3 (3%) 0 100 100
All All 2046/2458 (83%) 1975 (96%) 71 (4%) 0 100 100
There are no Ramachandran outliers to report.
5.3.2 Protein sidechains iO
In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all EMentries.
The Analysed column shows the number of residues for which the sidechain conformation wasanalysed, and the total number of residues.
Mol Chain Analysed Rotameric Outliers Percentiles
1 A 121/167 (72%) 121 (100%) 0 100 100
1 B 116/167 (70%) 116 (100%) 0 100 100Continued on next page...
Page 24 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Continued from previous page...
Mol Chain Analysed Rotameric Outliers Percentiles
1 C 100/167 (60%) 100 (100%) 0 100 100
1 D 119/167 (71%) 119 (100%) 0 100 100
1 E 121/167 (72%) 121 (100%) 0 100 100
1 F 100/167 (60%) 100 (100%) 0 100 100
2 G 205/209 (98%) 204 (100%) 1 (0%) 88 94
2 H 204/209 (98%) 204 (100%) 0 100 100
3 I 215/220 (98%) 215 (100%) 0 100 100
3 J 215/220 (98%) 215 (100%) 0 100 100
4 K 82/84 (98%) 82 (100%) 0 100 100
4 L 82/84 (98%) 82 (100%) 0 100 100
All All 1680/2028 (83%) 1679 (100%) 1 (0%) 93 97
All (1) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type2 G 197 MET
Some sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (12) suchsidechains are listed below:
Mol Chain Res Type1 A 2 GLN1 A 88 GLN1 B 88 GLN1 B 91 ASN1 B 149 GLN1 C 135 GLN1 D 2 GLN2 G 191 ASN3 I 191 ASN3 I 226 HIS3 J 191 ASN3 J 226 HIS
5.3.3 RNA iO
There are no RNA molecules in this entry.
Page 25 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
5.4 Non-standard residues in protein, DNA, RNA chains iO
There are no non-standard protein/DNA/RNA residues in this entry.
5.5 Carbohydrates iO
There are no monosaccharides in this entry.
5.6 Ligand geometry iO
2 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 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 LinkBond lengths Bond angles
Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2
6 PEF G 302 - 43,43,46 1.06 2 (4%) 47,48,51 0.93 2 (4%)
6 PEF G 301 - 43,43,46 1.06 2 (4%) 47,48,51 0.91 2 (4%)
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 Rings6 PEF G 302 - - 27/45/45/50 -
6 PEF G 301 - - 24/45/45/50 -
All (4) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)6 G 302 PEF O2-C10 3.68 1.44 1.346 G 301 PEF O2-C10 3.62 1.44 1.346 G 302 PEF O3-C30 2.67 1.41 1.336 G 301 PEF O3-C30 2.67 1.41 1.33
All (4) bond angle outliers are listed below:
Page 26 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)6 G 302 PEF O2-C10-C11 3.88 119.87 111.506 G 301 PEF O2-C10-C11 3.84 119.77 111.506 G 301 PEF O3-C30-C31 2.67 120.29 111.916 G 302 PEF O3-C30-C31 2.64 120.20 111.91
There are no chirality outliers.
All (51) torsion outliers are listed below:
Mol Chain Res Type Atoms6 G 302 PEF C31-C30-O3-C36 G 302 PEF O5-C30-O3-C36 G 301 PEF C31-C30-O3-C36 G 301 PEF O5-C30-O3-C36 G 301 PEF C34-C35-C36-C376 G 302 PEF C36-C37-C38-C396 G 301 PEF C17-C18-C19-C206 G 301 PEF C10-C11-C12-C136 G 302 PEF C11-C12-C13-C146 G 301 PEF C39-C40-C41-C426 G 302 PEF C21-C22-C23-C246 G 302 PEF C39-C40-C41-C426 G 302 PEF C12-C13-C14-C156 G 301 PEF C38-C39-C40-C416 G 302 PEF C31-C32-C33-C346 G 301 PEF C12-C13-C14-C156 G 301 PEF C21-C22-C23-C246 G 302 PEF C34-C35-C36-C376 G 301 PEF C42-C43-C44-C456 G 301 PEF C11-C10-O2-C26 G 302 PEF C42-C43-C44-C456 G 301 PEF C31-C32-C33-C346 G 302 PEF C35-C36-C37-C386 G 302 PEF O3P-C1-C2-O26 G 302 PEF C22-C23-C24-C256 G 301 PEF O2-C2-C3-O36 G 301 PEF C22-C23-C24-C256 G 302 PEF C10-C11-C12-C136 G 301 PEF C35-C36-C37-C386 G 302 PEF C38-C39-C40-C416 G 301 PEF O4-C10-O2-C26 G 301 PEF C36-C37-C38-C396 G 301 PEF C1-C2-C3-O36 G 302 PEF O3P-C1-C2-C3
Continued on next page...
Page 27 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
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Mol Chain Res Type Atoms6 G 302 PEF C16-C17-C18-C196 G 301 PEF C14-C15-C16-C176 G 302 PEF C15-C16-C17-C186 G 302 PEF O2-C2-C3-O36 G 302 PEF C14-C15-C16-C176 G 302 PEF C13-C14-C15-C166 G 301 PEF C40-C41-C42-C436 G 301 PEF O3P-C1-C2-O26 G 302 PEF C30-C31-C32-C336 G 302 PEF C32-C33-C34-C356 G 302 PEF C1-C2-C3-O36 G 302 PEF C33-C34-C35-C366 G 301 PEF O3P-C1-C2-C36 G 301 PEF O2-C10-C11-C126 G 302 PEF O2-C10-C11-C126 G 301 PEF O4-C10-C11-C126 G 302 PEF O4-C10-C11-C12
There are no ring outliers.
2 monomers are involved in 9 short contacts:
Mol Chain Res Type Clashes Symm-Clashes6 G 302 PEF 6 06 G 301 PEF 3 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 identi�ed 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 identi�ed 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-identi�ed 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 �nd su�cientequivalents in the CSD to analyse the geometry.
Page 28 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
Ligand PEF G 302
Bond lengths Bond angles
Torsions Rings
Ligand PEF G 301
Bond lengths Bond angles
Torsions Rings
5.7 Other polymers iO
There are no such residues in this entry.
5.8 Polymer linkage issues iO
There are no chain breaks in this entry.
Page 29 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
6 Map visualisation iO
This section contains visualisations of the EMDB entry EMD-22116. These are intended to permitvisual inspection of the internal detail of the map and identi�cation of artifacts.
6.1 Orthogonal projections iO
X Y Z
The images above show the map projected in three orthogonal projections, in greyscale.
6.2 Central slices iO
X Y Z
The images above show central slices of the map in three orthogonal directions, in greyscale.
Page 30 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
6.3 Largest variance slices iO
X Index: 162 Y Index: 144 Z Index: 198
The images above show the highest variance slices of the map in three orthogonal directions, ingreyscale.
6.4 Orthogonal surface views iO
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 0.27.This in conjunction with the slice images can indicate whether an appropriate contour level hasbeen selected.
6.5 Mask visualisation iO
This section was not generated. No masks were provided.
Page 31 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
7 Map analysis iO
This section contains the results of statistical analysis of the map.
7.1 Map-value distribution iO
The map-value distribution is plotted in 128 intervals along the x-axis. The y-axis is logarithmic.A spike in this graph at zero usually indicates that the volume has been masked.
Page 32 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
7.2 Volume estimate iO
The volume at the recommended contour level is 132 nm3; this corresponds to an approximatemass of 120 kDa.
The volume estimate graph shows how the enclosed volume varies with the contour level. Therecommended contour level is shown as a vertical line and the intersection between the line andthe curve gives the volume of the enclosed surface at the given level.
Page 33 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
7.3 Rotationally averaged power spectrum iO
Page 34 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
8 Fourier-Shell correlation iO
This section was not generated. No FSC curve or half maps provided.
Page 35 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
9 Map-model �t iO
This section contains information regarding the �t between EMDB map EMD-22116 and PDBmodel 6XBD. Per-residue inclusion information can be found in section 3 on page 9.
9.1 Map-model overlay iO
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 0.27 at50% transparency in yellow overlaid with a ribbon representation of the model coloured in blue.These images allow for the visual assessment of the quality of �t between the atomic model andthe map.
Page 36 Full wwPDB EM Map/Model Validation Report EMD-22116, 6XBD
9.2 Atom inclusion iO
At the recommended contour level, 88% of all backbone atoms, 84% of all non-hydrogen atoms,are inside the map.