full wwpdb em validation report i · 2020. 12. 21. · page3 fullwwpdbemvalidationreport...
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Full wwPDB EM Validation Report i○
Dec 21, 2020 – 12:28 AM EST
PDB ID : 6W6VEMDB ID : EMD-21564
Title : Structure of yeast RNase MRP holoenzymeAuthors : Perederina, A.; Li, D.; Lee, H.; Bator, C.; Berezin, I.; Hafenstein, S.L.; Krasil-
nikov, A.S.Deposited on : 2020-03-17
Resolution : 3.00 Å(reported)
This is a Full wwPDB EM Validation Report for a publicly released PDB entry.
We welcome your comments at [email protected] user guide is available at
https://www.wwpdb.org/validation/2017/EMValidationReportHelpwith 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:
EMDB validation analysis : 0.0.0.dev61MolProbity : 4.02b-467
Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Ideal geometry (proteins) : Engh & Huber (2001)
Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.16
https://www.wwpdb.org/validation/2017/EMValidationReportHelphttps://www.wwpdb.org/validation/2017/EMValidationReportHelphttps://www.wwpdb.org/validation/2017/EMValidationReportHelphttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#references
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Page 2 Full wwPDB EM Validation Report EMD-21564, 6W6V
1 Overall quality at a glance i○
The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY
The reported resolution of this entry is 3.00 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 158937 4297
Ramachandran outliers 154571 4023Sidechain outliers 154315 3826RNA backbone 4643 859
The table below summarises the geometric issues observed across the polymeric chains and their fitto the map. The red, orange, yellow and green segments of the bar indicate the fraction of residuesthat contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A greysegment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions
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Page 3 Full wwPDB EM Validation Report EMD-21564, 6W6V
Continued from previous page...Mol Chain Length Quality of chain
8 I 293
8 J 293
9 K 198
10 L 201
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Page 4 Full wwPDB EM Validation Report EMD-21564, 6W6V
2 Entry composition i○
There are 10 unique types of molecules in this entry. The entry contains 24850 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 RNA chain called RNA component of RNase MRP NME1.
Mol Chain Residues Atoms AltConf Trace
1 A 294 Total C N O P6261 2805 1097 2064 295 1 0
• Molecule 2 is a protein called Ribonucleases P/MRP protein subunit POP1.
Mol Chain Residues Atoms AltConf Trace
2 B 780 Total C N O S6345 4015 1154 1140 36 0 0
• Molecule 3 is a protein called RNases MRP/P 32.9 kDa subunit.
Mol Chain Residues Atoms AltConf Trace
3 D 212 Total C N O S1759 1131 300 320 8 0 0
• Molecule 4 is a protein called Ribonuclease P/MRP protein subunit POP5.
Mol Chain Residues Atoms AltConf Trace
4 E 169 Total C N O S1335 837 237 253 8 0 0
• Molecule 5 is a protein called Ribonucleases P/MRP protein subunit POP6.
Mol Chain Residues Atoms AltConf Trace
5 F 158 Total C N O S1280 809 223 243 5 0 0
• Molecule 6 is a protein called Ribonucleases P/MRP protein subunit POP7.
Mol Chain Residues Atoms AltConf Trace
6 G 126 Total C N O S1006 635 177 192 2 0 0
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#entry_composition
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Page 5 Full wwPDB EM Validation Report EMD-21564, 6W6V
• Molecule 7 is a protein called Ribonucleases P/MRP protein subunit POP8.
Mol Chain Residues Atoms AltConf Trace
7 H 125 Total C N O S1033 655 169 207 2 0 0
• Molecule 8 is a protein called Ribonuclease P/MRP protein subunit RPP1.
Mol Chain Residues Atoms AltConf Trace
8 I 243 Total C N O S1891 1194 342 346 9 0 0
8 J 293 Total C N O S2260 1415 413 422 10 0 0
• Molecule 9 is a protein called Ribonuclease MRP protein subunit SNM1.
Mol Chain Residues Atoms AltConf Trace
9 K 79 Total C N O S648 411 117 116 4 0 0
• Molecule 10 is a protein called Ribonuclease MRP protein subunit RMP1.
Mol Chain Residues Atoms AltConf Trace
10 L 121 Total C N O S1032 665 189 172 6 0 0
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Page 6 Full wwPDB EM Validation Report EMD-21564, 6W6V
3 Residue-property plots i○
These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. Thefirst 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 fit 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: RNA component of RNase MRP NME1
Chain A:
A A2 U3 C4 C5 A6 U7 G8 A9 C10
G15
A16
A26
U35
U36
A37
C38
A39
A40
U43
G44
G45
A49
A50
A51
A52
U U U U U57
A65
G66
U67
A68
A71
U72
G73
G78
G79
G80
U81
U82
G83
A84
A85
A86
A98
U99
U100
C101
G102
U103
A104
U105
G109
A112
G122
A123
U124
U125
A131
U U U U A A A U U G U U U144
A147
C154
A155
U156
U157
A158
A159
G160
G161
A162
G163
G164
A165
U166
G167
C168
C169
C U U G G174
G175
U176
A177
U178
U179
C180
C183
U184
U185
C186
U187
U188
G189
A190
U200
C201
U202
A U U G C A208
U212
A213
U218
G219
U U U U C U225
U226
C227
A231
C232
U233
G241
U U U G U A247
A251
A252
U253
C254
U255
A256
A257
A258
C259
C260
U266
A267
U268
G269
A270
C271
U278
C283
C284
C G U G C U290
U294
A300
C303
C304
A305
A306
U319
�U3
20C3
21U3
22
G325
A329
A333
U334
U335
C A C C C
• Molecule 2: Ribonucleases P/MRP protein subunit POP1
Chain B:
MET
SER
GLY
SER
LEU
SER
ARG
GLY
ASN
GLY
GLY
LYS
LYS
VAL
LEU
ASN
LYS
ASN
GLN
LEU
LEU
LYS
ARG
ASN
ARG
ILE
ARG
ASN
ALA
ARG
SER
ILE
ARG
ALA
GLU
ALA
VAL
ALA
ALA
SER
SER
THR
LYS
THR
GLY
THR
PRO
SER
ASP
LEU
SER
GLU
SER
GLY
SER
LYS
LEU
ASN
VAL
ASP
GLN
PHE
ILE
SER
SER
ARG
GLN
PHE
GLU
VAL
K71
�
Q74
H78
S84
�S8
5T8
6R8
7
L92
K95
R111
M112
R113
N114
R115
A116
D124
GLN
GLN
ASP
VAL
LEU
LYS
GLY
SER
SER
ALA
SER
SER
ARG
K138
N143
L147
Y148
M152
L156
L157
R158
P171
P172
N178
C179
H180
V181
R182
Q183
T187
L188
K189
N199
L204
L205
T215
I223
T242
T272
D289
T318
A319
E320
R321
Q335
S340
E343
E344
N345
�G3
46�
E347
D348
L353
C356
D357
V358
V361
R369
L370
H371
P372
T376
Q377
V378
F379
N380
I381
L382
L383
K386
A399
L409
M433
I434
T435
D436
L440
P441
H455
D464
�S4
65�
L476
P483
I487
F491
L494
R500
R517
L520
L521
V533
R549
R550
L551
K552
T553
R554
D555
W556
I557
L565
I589
F598
Y602
R626
K627
E636
K637
I641
L646
S650
S659
R662
F663
L664
Q665
I666
L667
R668
Y673
R676
K679
L683
K688
Q691
PHE
ASN
ALA
Q695
R698
D699
I700
N701
C702
V703
N704
D705
E708
S723
�I7
24E7
25E7
26N7
27I7
28P7
29
F740
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#residue_plots
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Page 7 Full wwPDB EM Validation Report EMD-21564, 6W6V
ARG
THR
PRO
ASP
SER
ILE
SER
VAL
ASN
S750
S751
�
F758
P759
R760
C761
I762
L769
L770
E771
R772
P775
Q783
H808
D819
L820
T828
Y829
H830
L831
N832
F841
T852
R853
N863
L867
V875
• Molecule 3: RNases MRP/P 32.9 kDa subunit
Chain D:
MET
ASP
ARG
THR
GLN
THR
PHE
ILE
LYS
ASP
CYS
LEU
PHE
THR
LYS
CYS
LEU
GLU
ASP
PRO
GLU
LYS
PRO
PHE
ASN
GLU
ASN
ARG
PHE
GLN
ASP
THR
LEU
LEU
LEU
LEU
PRO
THR
ASP
GLY
GLY
LEU
THR
SER
ARG
LEU
GLN
ARG
GLN
GLN
ARG
LYS
SER
LYS
LEU
ASN
LEU
ASP
ASN
LEU
GLN
LYS
VAL
SER
GLN
LEU
GLU
S68
�A6
9�
D70
�K7
1�
R76
D77
Y78
I81
N84
R90
E91
H120
E124
V137
P141
K144
L155
S167
L170
L173
S174
M175
L182
L183
R184
V185
L193
G198
W202
D203
K226
I236
S237
D238
D239
�D2
40�
S257
Y275
Q278
N279
• Molecule 4: Ribonuclease P/MRP protein subunit POP5
Chain E:
MET
V2 R3 I9 F15
D19
E24
�
K28
I31
L32
R37
Y63
A66
L74
S78
T81
I86
E91
M101
K105
I106
L112
H148
�L1
49�
S150
D151
�
I155
�
K161
R164
�E1
65�
N166
�E1
67N1
68E1
69�
N170
�GL
UAS
PAS
P
• Molecule 5: Ribonucleases P/MRP protein subunit POP6
Chain F:
M1 I16
R24
E28
I44
Q45
Y46
H47
N54
I55
K56
K57
S58
V59
I66
N67
M68
�A6
9�
D70
�
V78
I81
F82
I94
F98
Y102
I103
K104
Q111
S117
I120
K121
R122
E131
R132
V139
D144
I148
D149
L150
Q158
• Molecule 6: Ribonucleases P/MRP protein subunit POP7
Chain G:
MET
ALA
LEU
LYS
LYS
N6 N9�
K10
S11
R14
V15
T16
L24
T25
H26
K46
L66
G67
M68
G69
V72
E73
K74
C80
L100
E106
GLY
GLN
ALA
ASP
ILE
ASP
MET
GLU
SER
D116
D121
K122
E123
V140
• Molecule 7: Ribonucleases P/MRP protein subunit POP8
Chain H:
MET
GLY
LYS
K4 K13
L14
S15
K43
Y46
E51
E54
Y55
S56
D62
K63
L64
A65
Y66
I67
R68
V69
N70
H71
K74
D75
T76
S79
S86
T87
L90
�V9
1
P94
L95
T96
V97
E110
V111
T112
R116
L117
K121
�
E126
�E1
27Q1
28AS
P
CYS
LYS
CYS
ILE
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Page 8 Full wwPDB EM Validation Report EMD-21564, 6W6V
• Molecule 8: Ribonuclease P/MRP protein subunit RPP1
Chain I:
M1 D16
K17
K28
H34
M35
L36
T39
H40
N44
D64
R67
E71
D74
R75
T76
G77
L78
R83
P91
I106
A109
L119
N123
L124
D125
I126
Y133
L141
K142
H143
K144
E157
D166
V167
V177
R178
S179
V180
I181
R182
S186
C201
R202
G206
S209
D219
R220
K223
N235
R239
H243
LYS
GLN
THR
ILE
VAL
THR
GLY
GLY
GLY
SER
GLY
ASN
GLY
ASP
ASP
VAL
VAL
ASN
ASP
VAL
GLN
GLY
ILE
ASP
ASP
VAL
GLN
THR
ILE
LYS
VAL
VAL
LYS
ARG
SER
MET
ASP
ALA
GLU
GLN
LEU
GLY
HIS
ALA
SER
LYS
ARG
HIS
LYS
PRO
• Molecule 8: Ribonuclease P/MRP protein subunit RPP1
Chain J:
M1 L2 V3 D4 L5 N6 D16
�
T29
L33
H34
Y38
T39
H40
N44
F45
N48
K52
N55
D56
L60
N61
D64
I65
K66
R67
L78
K79
L80
R83
I84
T85
L86
I87
K93
G94
Q95
I100
F104
D105
I106
V107
A108
S120
L124
L128
L129
T130
K144
E157
R171
R178
I181
S186
R187
S193
L210
L216
R220
A229
T246
I247
V269
Q270
S278
�M2
79
H286
R290
P293
�
• Molecule 9: Ribonuclease MRP protein subunit SNM1
Chain K:
MET
ASN
K3 A6�
N19
V23
S33
G34
L35
Y36
Y37
H41
V44
Y47
Q48
L55
�
C66
V67
Y68
V69
P70
L78
T79
T80
N81
THR
GLU
GLN
GLY
ASP
SER
ASP
GLU
LEU
GLY
GLY
GLU
SER
MET
GLU
GLY
PRO
LYS
LYS
CYS
ILE
GLN
VAL
ASN
CYS
LEU
ASN
CYS
GLU
LYS
SER
LYS
LEU
PHE
GLU
TRP
LYS
SER
GLU
PHE
VAL
VAL
PRO
THR
PHE
GLY
GLN
ASP
VAL
SER
PRO
MET
ILE
ASN
SER
THR
SER
SER
GLY
LYS
VAL
SER
TYR
ALA
VAL
LYS
LYS
PRO
GLN
LYS
SER
LYS
THR
SER
THR
GLY
LYS
GLU
ARG
SER
LYS
LYS
ARG
LYS
LEU
ASN
SER
LEU
THR
ASN
LEU
LEU
SER
LYS
ARG
ASN
GLN
GLU
LYS
LYS
MET
GLU
LYS
LYS
LYS
SER
SER
SER
LEU
SER
LEU
GLU
SER
PHE
MET
LYS
SER
• Molecule 10: Ribonuclease MRP protein subunit RMP1
Chain L:
M1 D2 E3�
M4 D5 N6 R9 S10
�L1
1E1
2
R16
N22
K26
G36
R43
S53
SER
ARG
ARG
LEU
GLN
ALA
LYS
R61
L62
K63
L74
K83
R84
L101
L105
N111
M117
W120
I128
ARG
CYS
GLY
CYS
LEU
ILE
LYS
ASN
LEU
PRO
ARG
THR
LYS
ALA
LYS
SER
VAL
VAL
ASN
ASP
VAL
GLU
GLU
LEU
GLY
GLU
ILE
ILE
ASP
GLU
ASP
ILE
GLY
ASN
ASN
VAL
GLN
GLU
ASN
GLU
LEU
VAL
ILE
THR
SER
ILE
PRO
LYS
PRO
LEU
THR
GLU
ASN
CYS
LYS
LYS
LYS
LYS
LYS
ARG
LYS
LYS
LYS
ASN
LYS
SER
ALA
ILE
ASP
GLY
ILE
PHE
GLY
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Page 9 Full wwPDB EM Validation Report EMD-21564, 6W6V
4 Experimental information i○
Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, Not providedNumber of particles used 155205 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) 39 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector FEI FALCON III (4k x 4k) DepositorMaximum map value 3.131 DepositorMinimum map value -1.597 DepositorAverage map value -0.000 DepositorMap value standard deviation 0.094 DepositorRecommended contour level 0.3 DepositorMap size (Å) 340.48, 340.48, 340.48 wwPDBMap dimensions 512, 512, 512 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 0.665, 0.665, 0.665 Depositor
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#experimental_info
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Page 10 Full wwPDB EM Validation Report EMD-21564, 6W6V
5 Model quality i○
5.1 Standard geometry i○
The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
Mol Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >51 A 0.35 0/6993 0.76 0/108702 B 0.29 0/6483 0.47 1/8734 (0.0%)3 D 0.28 0/1790 0.47 0/24014 E 0.28 0/1351 0.45 0/18145 F 0.27 0/1298 0.48 0/17436 G 0.28 0/1019 0.55 1/1368 (0.1%)7 H 0.28 0/1055 0.47 0/14288 I 0.27 0/1919 0.49 0/25928 J 0.26 0/2291 0.46 0/30929 K 0.27 0/662 0.53 0/89110 L 0.28 0/1053 0.43 0/1418All All 0.30 0/25914 0.58 2/36351 (0.0%)
There are no bond length outliers.
All (2) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)6 G 66 LEU CA-CB-CG 6.26 129.70 115.302 B 626 ARG CA-CB-CG 5.15 124.73 113.40
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.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#model_qualityhttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#standard_geometryhttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#close_contacts
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Page 11 Full wwPDB EM Validation Report EMD-21564, 6W6V
Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes1 A 6261 0 3165 59 02 B 6345 0 6427 94 03 D 1759 0 1817 21 04 E 1335 0 1380 21 05 F 1280 0 1317 17 06 G 1006 0 1048 14 07 H 1033 0 986 22 08 I 1891 0 1982 30 08 J 2260 0 2351 41 09 K 648 0 649 11 010 L 1032 0 1048 17 0All All 24850 0 22170 304 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 6.
All (304) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)1:A:167:G:H1 1:A:176:U:H3 1.28 0.805:F:47:HIS:HB3 5:F:81:ILE:HG22 1.65 0.791:A:79:G:H22 4:E:3:ARG:HH22 1.34 0.751:A:164:G:H1 1:A:179:U:H3 1.35 0.75
8:J:130:THR:HG22 8:J:157:GLU:HB3 1.71 0.731:A:303:C:OP2 8:J:187:ARG:NH2 2.22 0.73
2:B:521:LEU:HD13 10:L:74:LEU:HD21 1.71 0.713:D:90:ARG:NH1 3:D:91:GLU:OE2 2.23 0.704:E:91:GLU:OE2 8:J:178:ARG:NH1 2.24 0.702:B:494:LEU:O 2:B:500:ARG:NH1 2.24 0.69
2:B:242:THR:OG1 2:B:289:ASP:OD2 2.10 0.699:K:33:SER:OG 9:K:69:VAL:O 2.09 0.69
2:B:361:VAL:HG21 2:B:491:PHE:CE2 2.29 0.688:J:269:VAL:HG13 8:J:270:GLN:HG3 1.75 0.688:I:142:LYS:HE2 8:I:144:LYS:HD2 1.76 0.681:A:233:U:OP2 10:L:84:ARG:NH2 2.27 0.681:A:157:U:OP2 2:B:111:ARG:NH2 2.28 0.674:E:63:TYR:HB2 7:H:46:TYR:HE1 1.60 0.6610:L:5:ASP:O 10:L:9:ARG:NH1 2.29 0.66
2:B:550:ARG:HD3 2:B:557:ILE:HD11 1.78 0.662:B:668:ARG:NH2 2:B:820:LEU:O 2.29 0.66
7:H:71:HIS:O 7:H:74:LYS:NZ 2.28 0.656:G:14:ARG:NH1 6:G:16:THR:OG1 2.30 0.65
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Page 12 Full wwPDB EM Validation Report EMD-21564, 6W6V
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)2:B:828:THR:HG22 2:B:829:TYR:H 1.61 0.652:B:550:ARG:NH2 2:B:555:ASP:OD2 2.29 0.645:F:122:ARG:NH2 5:F:131:GLU:OE2 2.31 0.644:E:168:ASN:ND2 4:E:168:ASN:O 2.28 0.641:A:290:U:O2 2:B:637:LYS:NZ 2.31 0.63
2:B:783:GLN:NE2 2:B:819:ASP:OD1 2.29 0.638:I:219:ASP:O 8:I:223:LYS:NZ 2.31 0.63
10:L:12:GLU:HG2 10:L:16:ARG:HH12 1.63 0.632:B:665:GLN:NE2 2:B:758:PHE:O 2.32 0.621:A:231:A:OP2 10:L:43:ARG:NH2 2.32 0.628:I:71:GLU:OE1 8:I:75:ARG:NH1 2.32 0.626:G:69:GLY:O 6:G:72:VAL:HG12 1.99 0.621:A:185:U:OP1 2:B:199:ASN:ND2 2.33 0.621:A:37:A:H2’ 6:G:68:MET:HG2 1.82 0.61
8:J:44:ASN:OD1 8:J:45:PHE:N 2.33 0.6110:L:2:ASP:OD1 10:L:6:ASN:ND2 2.33 0.612:B:673:TYR:OH 2:B:676:ARG:NH2 2.33 0.607:H:75:ASP:OD1 7:H:76:THR:N 2.33 0.602:B:357:ASP:HB2 2:B:369:ARG:HB2 1.84 0.603:D:184:ARG:NH1 8:J:279:MET:HG2 2.17 0.60
2:B:71:LYS:N 10:L:111:ASN:HD21 2.00 0.601:A:218:U:O4 2:B:179:CYS:N 2.35 0.59
8:J:181:ILE:HG23 8:J:186:SER:HB3 1.84 0.591:A:15:G:OP1 2:B:627:LYS:NZ 2.35 0.591:A:266:U:O2’ 1:A:306:A:N6 2.35 0.588:J:120:SER:HA 8:J:124:LEU:HD12 1.84 0.581:A:40:A:H61 6:G:11:SER:HB3 1.68 0.588:I:91:PRO:HA 8:I:119:LEU:HD22 1.86 0.581:A:218:U:O4 2:B:180:HIS:N 2.35 0.58
2:B:434:ILE:HG13 2:B:440:LEU:HD21 1.85 0.582:B:215:THR:HG21 2:B:500:ARG:HH21 1.69 0.582:B:729:PRO:HG2 2:B:761:CYS:HA 1.86 0.582:B:178:ASN:O 2:B:182:ARG:NE 2.32 0.572:B:441:PRO:O 2:B:549:ARG:NH2 2.37 0.574:E:19:ASP:O 8:I:28:LYS:NZ 2.36 0.57
2:B:204:LEU:HG 2:B:205:LEU:H 1.68 0.572:B:434:ILE:HG22 2:B:436:ASP:H 1.70 0.579:K:41:HIS:HA 9:K:44:VAL:HG12 1.87 0.578:I:34:HIS:HB2 8:I:78:LEU:HD13 1.87 0.57
8:J:85:THR:HG22 8:J:108:ALA:HB3 1.87 0.562:B:319:ALA:O 2:B:321:ARG:N 2.37 0.56
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Page 13 Full wwPDB EM Validation Report EMD-21564, 6W6V
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)8:I:206:GLY:O 8:I:209:SER:OG 2.19 0.561:A:212:U:H2’ 1:A:213:A:H8 1.70 0.56
2:B:476:LEU:HD11 6:G:100:LEU:HD21 1.87 0.5610:L:12:GLU:O 10:L:16:ARG:NH1 2.39 0.565:F:82:PHE:HB3 5:F:139:VAL:HG12 1.88 0.56
2:B:769:LEU:HD11 2:B:775:PRO:HD3 1.88 0.568:J:64:ASP:OD2 8:J:67:ARG:NH2 2.34 0.567:H:90:LEU:HD12 7:H:91:VAL:HG13 1.88 0.562:B:84:SER:OG 2:B:85:SER:N 2.39 0.558:I:201:CYS:O 8:I:202:ARG:NH1 2.30 0.558:J:286:HIS:O 8:J:290:ARG:NH1 2.39 0.552:B:455:HIS:O 2:B:517:ARG:NH2 2.39 0.55
4:E:106:ILE:HD12 4:E:112:LEU:HD11 1.87 0.557:H:86:SER:OG 7:H:87:THR:N 2.38 0.551:A:218:U:C4 2:B:180:HIS:HB3 2.41 0.55
2:B:727:ASN:OD1 2:B:728:ILE:HG12 2.06 0.558:J:3:VAL:HG12 8:J:40:HIS:HB2 1.88 0.555:F:24:ARG:O 5:F:28:GLU:HG2 2.07 0.542:B:74:GLN:O 2:B:78:HIS:ND1 2.40 0.54
2:B:646:LEU:HD21 2:B:683:LEU:HD23 1.88 0.542:B:204:LEU:O 2:B:205:LEU:HG 2.08 0.534:E:105:LYS:O 4:E:105:LYS:HD2 2.07 0.539:K:78:LEU:HG 9:K:80:THR:H 1.73 0.532:B:182:ARG:O 2:B:183:GLN:HG3 2.07 0.531:A:158:A:H2’ 1:A:159:A:H8 1.74 0.53
2:B:683:LEU:HA 2:B:703:VAL:HG12 1.91 0.537:H:62:ASP:OD1 7:H:62:ASP:N 2.42 0.532:B:113:ARG:NH2 2:B:114:ASN:OD1 2.42 0.531:A:161:G:H2’ 1:A:162:A:H8 1.74 0.53
5:F:55:ILE:HG13 5:F:94:ILE:HG12 1.90 0.531:A:73:G:O6 6:G:46:LYS:NZ 2.35 0.53
8:I:64:ASP:OD1 8:I:67:ARG:HB3 2.09 0.5310:L:117:MET:O 10:L:120:TRP:N 2.43 0.522:B:762:ILE:HD12 2:B:841:PHE:HB3 1.91 0.522:B:183:GLN:HA 2:B:187:THR:HB 1.92 0.521:A:158:A:H2’ 1:A:159:A:C8 2.44 0.524:E:168:ASN:C 4:E:168:ASN:HD22 2.11 0.528:J:2:LEU:HB3 8:J:38:TYR:HD1 1.74 0.528:J:34:HIS:HB2 8:J:78:LEU:HD11 1.91 0.527:H:54:GLU:OE2 8:I:179:SER:OG 2.20 0.528:J:60:LEU:HD23 8:J:100:ILE:HD12 1.91 0.52
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Page 14 Full wwPDB EM Validation Report EMD-21564, 6W6V
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)8:J:55:ASN:OD1 8:J:56:ASP:N 2.43 0.522:B:433:MET:SD 2:B:464:ASP:HB3 2.50 0.512:B:335:GLN:NE2 2:B:550:ARG:HD2 2.23 0.518:J:48:ASN:HA 8:J:87:ILE:HB 1.90 0.513:D:84:ASN:ND2 9:K:67:VAL:O 2.42 0.511:A:50:A:H2’ 1:A:51:A:C8 2.45 0.51
8:J:6:ASN:OD1 8:J:83:ARG:NH1 2.43 0.512:B:399:ALA:HB1 2:B:565:LEU:HD22 1.92 0.511:A:256:A:H5” 2:B:87:ARG:HH12 1.76 0.511:A:176:U:H2’ 1:A:177:A:C8 2.46 0.51
2:B:662:ARG:HH22 2:B:725:GLU:HB3 1.76 0.518:I:39:THR:OG1 8:I:40:HIS:ND1 2.38 0.517:H:15:SER:HB3 7:H:64:LEU:HA 1.93 0.511:A:109:G:N2 1:A:112:A:OP2 2.42 0.511:A:15:G:H2’ 1:A:83:G:N1 2.26 0.51
7:H:56:SER:HB2 7:H:68:ARG:HG2 1.94 0.508:I:235:ASN:O 8:I:239:ARG:HG2 2.12 0.50
7:H:54:GLU:OE1 8:I:182:ARG:NE 2.40 0.502:B:828:THR:HG22 2:B:829:TYR:N 2.26 0.50
1:A:83:G:H1’ 1:A:84:A:H4’ 1.94 0.508:I:201:CYS:SG 8:I:202:ARG:N 2.85 0.50
2:B:641:ILE:HD13 2:B:863:ASN:HB3 1.95 0.494:E:32:LEU:HA 8:I:35:MET:HE1 1.93 0.492:B:378:VAL:O 2:B:381:ILE:HB 2.13 0.49
8:J:33:LEU:HD12 8:J:38:TYR:HD2 1.77 0.492:B:318:THR:HG23 2:B:319:ALA:O 2.11 0.494:E:31:ILE:HG22 8:I:35:MET:HE3 1.95 0.493:D:144:LYS:HE3 3:D:182:LEU:HB2 1.95 0.497:H:75:ASP:O 7:H:79:SER:OG 2.15 0.491:A:8:G:H2’ 1:A:9:A:H8 1.78 0.49
8:J:40:HIS:CE1 8:J:79:LYS:HD2 2.48 0.491:A:154:C:H2’ 1:A:155:A:H8 1.77 0.49
2:B:272:THR:HG22 2:B:589:ILE:HD11 1.96 0.485:F:117:SER:OG 6:G:80:CYS:SG 2.66 0.482:B:171:PRO:HB2 2:B:172:PRO:HD3 1.95 0.488:I:166:ASP:OD1 8:I:167:VAL:N 2.47 0.488:J:3:VAL:HG21 8:J:229:ALA:HB3 1.96 0.488:J:6:ASN:OD1 8:J:44:ASN:ND2 2.25 0.483:D:137:VAL:O 3:D:141:PRO:HD3 2.12 0.484:E:28:LYS:O 4:E:32:LEU:HD13 2.14 0.481:A:164:G:H2’ 1:A:165:A:C8 2.49 0.47
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Page 15 Full wwPDB EM Validation Report EMD-21564, 6W6V
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)5:F:59:VAL:HG23 5:F:98:PHE:HB2 1.95 0.474:E:63:TYR:HB2 7:H:46:TYR:CE1 2.47 0.478:J:52:LYS:HA 8:J:95:GLN:NE2 2.28 0.479:K:47:TYR:O 9:K:48:GLN:HG2 2.15 0.475:F:54:ASN:O 5:F:57:LYS:HG3 2.14 0.471:A:232:C:N4 10:L:36:GLY:O 2.44 0.47
7:H:13:LYS:HG3 7:H:66:TYR:CE1 2.49 0.475:F:148:ILE:HG22 5:F:150:LEU:H 1.80 0.472:B:598:PHE:HA 2:B:602:TYR:CD1 2.50 0.4710:L:83:LYS:HD2 10:L:83:LYS:HA 1.71 0.472:B:383:LEU:HD22 2:B:386:LYS:HD3 1.97 0.472:B:673:TYR:CD2 2:B:700:ILE:HG21 2.51 0.462:B:483:PRO:O 2:B:487:ILE:HG12 2.15 0.462:B:830:HIS:NE2 2:B:832:ASN:HB2 2.30 0.46
1:A:5:C:H2’ 1:A:6:A:H8 1.80 0.468:I:44:ASN:HA 8:I:83:ARG:HG3 1.97 0.46
2:B:549:ARG:HB2 2:B:556:TRP:CZ3 2.50 0.468:I:16:ASP:OD1 8:I:17:LYS:N 2.48 0.469:K:66:CYS:HB2 9:K:68:TYR:CZ 2.51 0.469:K:68:TYR:HD1 9:K:70:PRO:HD3 1.80 0.461:A:160:G:H2’ 1:A:161:G:C8 2.49 0.464:E:78:SER:OG 4:E:81:THR:O 2.31 0.46
3:D:184:ARG:HH12 8:J:279:MET:HG2 1.80 0.463:D:182:LEU:HD12 3:D:198:GLY:O 2.15 0.46
8:I:123:ASN:O 8:I:124:LEU:HD22 2.15 0.464:E:66:ALA:HB2 8:J:171:ARG:HG2 1.97 0.46
1:A:8:G:H2’ 1:A:9:A:C8 2.51 0.462:B:371:HIS:CG 2:B:372:PRO:HD2 2.51 0.462:B:659:SER:OG 2:B:659:SER:O 2.34 0.458:I:177:VAL:HA 8:I:180:VAL:HG12 1.97 0.45
3:D:155:LEU:HD11 3:D:173:LEU:HD21 1.97 0.456:G:123:GLU:N 6:G:123:GLU:OE2 2.48 0.45
7:H:110:GLU:HG2 7:H:116:ARG:HG3 1.99 0.453:D:185:VAL:HG11 3:D:193:LEU:HD23 1.98 0.455:F:111:GLN:NE2 5:F:158:GLN:OE1 2.49 0.458:I:133:TYR:OH 8:I:157:GLU:O 2.21 0.45
8:J:246:THR:HG23 8:J:247:ILE:HG12 1.99 0.452:B:772:ARG:HE 2:B:808:HIS:CE1 2.34 0.457:H:96:THR:HG22 7:H:97:VAL:N 2.31 0.452:B:204:LEU:HG 2:B:205:LEU:N 2.32 0.458:J:33:LEU:HD12 8:J:38:TYR:CD2 2.51 0.45
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Page 16 Full wwPDB EM Validation Report EMD-21564, 6W6V
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)8:J:4:ASP:OD1 8:J:193:SER:OG 2.27 0.45
2:B:116:ALA:HB2 2:B:156:LEU:HD12 1.98 0.458:J:29:THR:O 8:J:33:LEU:HD23 2.17 0.451:A:160:G:N2 1:A:184:U:O2 2.49 0.454:E:9:ILE:HB 4:E:86:ILE:HG22 1.99 0.451:A:105:U:H3 2:B:156:LEU:HD21 1.82 0.451:A:190:A:OP2 2:B:158:ARG:NH1 2.50 0.455:F:44:ILE:HA 5:F:78:VAL:O 2.17 0.452:B:700:ILE:O 2:B:700:ILE:HG22 2.17 0.45
2:B:435:THR:HG21 6:G:24:LEU:HB2 1.99 0.452:B:550:ARG:HB2 2:B:555:ASP:OD1 2.16 0.443:D:167:SER:HA 3:D:170:LEU:HD12 1.99 0.448:I:202:ARG:HD3 8:I:202:ARG:HA 1.80 0.442:B:698:ARG:HH22 2:B:708:GLU:CD 2.21 0.443:D:77:ASP:OD1 3:D:78:TYR:N 2.50 0.445:F:102:TYR:OH 5:F:144:ASP:OD1 2.29 0.441:A:123:A:H5” 1:A:124:U:OP1 2.17 0.441:A:268:U:H5” 1:A:269:G:H5’ 1.99 0.44
2:B:520:LEU:HD11 2:B:533:VAL:HA 1.99 0.442:B:673:TYR:HD2 2:B:700:ILE:HG21 1.82 0.443:D:120:HIS:CE1 3:D:124:GLU:HG3 2.52 0.448:J:210:LEU:H 8:J:210:LEU:HD12 1.82 0.448:J:5:LEU:O 8:J:83:ARG:NH1 2.51 0.44
10:L:26:LYS:HA 10:L:26:LYS:HE2 1.99 0.442:B:760:ARG:HA 2:B:760:ARG:HD3 1.88 0.445:F:66:ILE:HD11 5:F:144:ASP:HB2 2.00 0.446:G:73:GLU:HG2 6:G:74:LYS:N 2.33 0.44
1:A:79:G:N2 4:E:3:ARG:HH22 2.08 0.434:E:101:MET:HE3 8:I:206:GLY:HA3 2.00 0.438:J:2:LEU:HB3 8:J:38:TYR:CD1 2.52 0.433:D:81:ILE:HD13 9:K:37:TYR:CE1 2.52 0.434:E:161:LYS:HA 4:E:161:LYS:HD2 1.80 0.438:I:83:ARG:HB3 8:I:106:ILE:HB 2.01 0.432:B:551:LEU:O 2:B:554:ARG:HG2 2.19 0.438:I:186:SER:O 8:I:220:ARG:NH2 2.51 0.43
3:D:184:ARG:CZ 8:J:279:MET:HG2 2.49 0.432:B:335:GLN:OE1 2:B:552:LYS:HB3 2.19 0.432:B:343:GLU:HA 2:B:348:ASP:CG 2.38 0.437:H:46:TYR:CD2 7:H:76:THR:HG23 2.53 0.431:A:161:G:N2 1:A:183:C:N3 2.66 0.43
7:H:54:GLU:HG3 7:H:70:ASN:HD21 1.82 0.43Continued on next page...
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Page 17 Full wwPDB EM Validation Report EMD-21564, 6W6V
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)8:J:216:LEU:HD11 8:J:220:ARG:HD2 2.00 0.435:F:45:GLN:OE1 5:F:45:GLN:N 2.52 0.437:H:86:SER:O 7:H:94:PRO:HB3 2.19 0.43
2:B:409:LEU:HA 2:B:409:LEU:HD23 1.79 0.433:D:175:MET:HG2 3:D:257:SER:O 2.19 0.438:J:83:ARG:HG2 8:J:106:ILE:HB 2.01 0.431:A:251:A:H2’ 1:A:252:A:C8 2.53 0.43
3:D:202:TRP:CE2 9:K:35:LEU:HD12 2.54 0.4310:L:22:ASN:O 10:L:26:LYS:HE3 2.19 0.431:A:212:U:H2’ 1:A:213:A:C8 2.50 0.42
8:I:109:ALA:HB2 8:I:126:ILE:HG21 2.01 0.429:K:66:CYS:HB2 9:K:68:TYR:CE1 2.53 0.4210:L:12:GLU:HG2 10:L:16:ARG:NH1 2.29 0.42
1:A:4:C:H2’ 1:A:5:C:C6 2.54 0.426:G:26:HIS:ND1 6:G:26:HIS:O 2.52 0.421:A:251:A:H2’ 1:A:252:A:H8 1.84 0.421:A:278:U:O2’ 1:A:322:U:OP1 2.33 0.422:B:705:ASP:O 2:B:708:GLU:HG3 2.20 0.424:E:15:PHE:HB3 4:E:37:ARG:CZ 2.49 0.421:A:164:G:H2’ 1:A:165:A:H8 1.84 0.422:B:683:LEU:O 2:B:702:CYS:HB3 2.20 0.42
2:B:688:LYS:HD2 2:B:688:LYS:HA 1.63 0.426:G:72:VAL:HG13 6:G:73:GLU:H 1.84 0.427:H:111:VAL:HG22 7:H:112:THR:HG23 2.01 0.422:B:356:CYS:SG 2:B:358:VAL:HG23 2.60 0.422:B:698:ARG:NH1 2:B:708:GLU:OE2 2.52 0.428:I:141:LEU:HD23 8:I:141:LEU:H 1.84 0.426:G:121:ASP:N 6:G:121:ASP:OD1 2.53 0.421:A:10:C:OP1 3:D:226:LYS:NZ 2.53 0.42
8:I:36:LEU:HD12 8:I:201:CYS:SG 2.60 0.428:I:74:ASP:C 8:I:76:THR:H 2.23 0.42
8:J:93:LYS:HD3 8:J:93:LYS:HA 1.87 0.421:A:3:U:H2’ 1:A:4:C:C6 2.55 0.421:A:51:A:H2’ 1:A:52:A:C8 2.55 0.421:A:5:C:H2’ 1:A:6:A:C8 2.55 0.42
3:D:237:SER:OG 3:D:238:ASP:N 2.51 0.423:D:275:TYR:HA 3:D:278:GLN:HB2 2.02 0.421:A:50:A:H2’ 1:A:51:A:H8 1.85 0.41
2:B:335:GLN:HE22 2:B:550:ARG:HD2 1.85 0.417:H:43:LYS:HB2 7:H:51:GLU:OE2 2.19 0.412:B:679:LYS:HD3 2:B:679:LYS:N 2.34 0.41
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Page 18 Full wwPDB EM Validation Report EMD-21564, 6W6V
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Atom-1 Atom-2 Interatomicdistance (Å)Clash
overlap (Å)3:D:203:ASP:N 3:D:203:ASP:OD1 2.42 0.41
2:B:770:LEU:HD12 2:B:867:LEU:HD23 2.02 0.412:B:663:PHE:CZ 2:B:667:LEU:HD22 2.56 0.417:H:46:TYR:CE2 7:H:76:THR:HG23 2.56 0.419:K:19:ASN:O 9:K:23:VAL:HG23 2.21 0.411:A:254:C:H2’ 1:A:255:U:C6 2.56 0.41
3:D:236:ILE:HG23 3:D:237:SER:N 2.36 0.418:J:61:ASN:HB3 8:J:104:PHE:CE1 2.56 0.412:B:852:THR:OG1 2:B:853:ARG:N 2.53 0.414:E:19:ASP:OD1 4:E:19:ASP:N 2.53 0.414:E:74:LEU:HD12 4:E:74:LEU:HA 1.89 0.415:F:104:LYS:HA 5:F:104:LYS:HD3 1.86 0.411:A:39:A:C6 1:A:65:A:C5 3.08 0.41
2:B:340:SER:HB3 2:B:353:LEU:HD11 2.02 0.4110:L:62:LEU:HD11 10:L:63:LYS:HE3 2.02 0.41
5:F:120:ILE:O 5:F:132:ARG:HA 2.20 0.412:B:143:ASN:HB3 2:B:147:LEU:HG 2.03 0.418:J:128:LEU:HA 8:J:128:LEU:HD23 1.97 0.41
1:A:9:A:H2’ 1:A:10:C:C6 2.55 0.402:B:376:THR:O 2:B:380:ASN:ND2 2.47 0.402:B:636:GLU:O 2:B:650:SER:OG 2.31 0.405:F:16:ILE:HG13 5:F:120:ILE:HD11 2.03 0.401:A:260:C:O2’ 2:B:95:LYS:HE2 2.22 0.40
8:J:65:ILE:HD13 8:J:80:LEU:HB3 2.04 0.4010:L:101:LEU:O 10:L:105:LEU:HD13 2.21 0.401:A:258:A:N6 2:B:92:LEU:HD23 2.37 0.401:A:49:A:H2’ 1:A:50:A:C8 2.57 0.402:B:223:ILE:H 2:B:223:ILE:HD12 1.86 0.40
6:G:14:ARG:HH11 6:G:14:ARG:HG2 1.86 0.401:A:78:G:O2’ 1:A:268:U:O2 2.33 0.40
7:H:117:LEU:HD23 7:H:117:LEU:HA 1.93 0.408:J:78:LEU:HD23 8:J:78:LEU:HA 1.91 0.408:J:40:HIS:ND1 8:J:79:LYS:HD2 2.36 0.402:B:148:TYR:CZ 2:B:152:MET:HG3 2.57 0.4010:L:22:ASN:O 10:L:26:LYS:HG2 2.21 0.40
There are no symmetry-related clashes.
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Page 19 Full wwPDB EM Validation Report EMD-21564, 6W6V
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
2 B 772/875 (88%) 690 (89%) 82 (11%) 0 100 100
3 D 210/279 (75%) 189 (90%) 21 (10%) 0 100 100
4 E 167/173 (96%) 146 (87%) 21 (13%) 0 100 100
5 F 156/158 (99%) 142 (91%) 14 (9%) 0 100 100
6 G 122/140 (87%) 113 (93%) 9 (7%) 0 100 100
7 H 123/133 (92%) 105 (85%) 18 (15%) 0 100 100
8 I 241/293 (82%) 211 (88%) 30 (12%) 0 100 100
8 J 291/293 (99%) 259 (89%) 32 (11%) 0 100 100
9 K 77/198 (39%) 64 (83%) 13 (17%) 0 100 100
10 L 117/201 (58%) 108 (92%) 9 (8%) 0 100 100
All All 2276/2743 (83%) 2027 (89%) 249 (11%) 0 100 100
There are no Ramachandran outliers to report.
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
2 B 704/785 (90%) 703 (100%) 1 (0%) 93 98
3 D 196/261 (75%) 195 (100%) 1 (0%) 88 96
4 E 156/160 (98%) 155 (99%) 1 (1%) 86 95
5 F 149/149 (100%) 147 (99%) 2 (1%) 69 89Continued on next page...
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#torsion_angleshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_backbonehttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_sidechains
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Continued from previous page...Mol Chain Analysed Rotameric Outliers Percentiles
6 G 116/127 (91%) 116 (100%) 0 100 100
7 H 116/123 (94%) 116 (100%) 0 100 100
8 I 217/258 (84%) 217 (100%) 0 100 100
8 J 258/258 (100%) 256 (99%) 2 (1%) 81 93
9 K 73/184 (40%) 73 (100%) 0 100 100
10 L 110/182 (60%) 110 (100%) 0 100 100
All All 2095/2487 (84%) 2088 (100%) 7 (0%) 92 97
All (7) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type2 B 189 LYS3 D 76 ARG4 E 168 ASN5 F 57 LYS5 F 132 ARG8 J 52 LYS8 J 144 LYS
Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (1) suchsidechains are listed below:
Mol Chain Res Type5 F 111 GLN
5.3.3 RNA i○
Mol Chain Analysed Backbone Outliers Pucker Outliers1 A 285/340 (83%) 67 (23%) 0
All (67) RNA backbone outliers are listed below:
Mol Chain Res Type1 A 16 A1 A 26 A1 A 35 U1 A 36 U1 A 39 A
Continued on next page...
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#rna
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Continued from previous page...Mol Chain Res Type1 A 40 A1 A 43 U1 A 44 G1 A 45 G1 A 52 A1 A 66 G1 A 67 U1 A 68 A1 A 71 A1 A 72 U1 A 79 G1 A 80 G1 A 81 U1 A 82 U1 A 83 G1 A 84 A1 A 85 A1 A 86 A1 A 98 A1 A 99 U1 A 100 U1 A 102 G1 A 104 A1 A 105 U1 A 122 G1 A 124 U1 A 125 U1 A 131 A1 A 147 A1 A 158 A1 A 166 U1 A 169 C1 A 180 C1 A 185 U1 A 186 C1 A 187 U1 A 188 U1 A 189 G1 A 190 A1 A 200 U1 A 201 C1 A 213 A
Continued on next page...
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Continued from previous page...Mol Chain Res Type1 A 218 U1 A 219 G1 A 227 C1 A 233 U1 A 256 A1 A 259 C1 A 260 C1 A 266 U1 A 271 C1 A 283 C1 A 294 U1 A 300 A1 A 303 C1 A 305 A1 A 319 U1 A 320 U1 A 325 G1 A 329 A1 A 333 A1 A 334 U
There are no RNA pucker outliers to report.
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 monosaccharides in this entry.
5.6 Ligand geometry i○
There are no ligands in this entry.
5.7 Other polymers i○
There are no such residues in this entry.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligandshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligands
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5.8 Polymer linkage issues i○
There are no chain breaks in this entry.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#polymer_linkage
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6 Map visualisation i○
This section contains visualisations of the EMDB entry EMD-21564. These allow visual inspectionof the internal detail of the map and identification of artifacts.
No raw map or half-maps were deposited for this entry and therefore no images, graphs, etc.pertaining to the raw map can be shown.
6.1 Orthogonal projections i○
6.1.1 Primary map
X Y Z
The images above show the map projected in three orthogonal directions.
6.2 Central slices i○
6.2.1 Primary map
X Index: 256 Y Index: 256 Z Index: 256
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_visualisationhttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_projectionshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#central_slices
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The images above show central slices of the map in three orthogonal directions.
6.3 Largest variance slices i○
6.3.1 Primary map
X Index: 267 Y Index: 256 Z Index: 260
The images above show the largest variance slices of the map in three orthogonal directions.
6.4 Orthogonal surface views i○
6.4.1 Primary map
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 0.3.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#largest_variance_sliceshttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_views
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6.5 Mask visualisation i○
This section was not generated. No masks/segmentation were deposited.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#masks
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7 Map analysis i○
This section contains the results of statistical analysis of the map.
7.1 Map-value distribution i○
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.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_analysishttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_value_distribution
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7.2 Volume estimate i○
The volume at the recommended contour level is 243 nm3; this corresponds to an approximatemass of 220 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.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#volume_estimate
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7.3 Rotationally averaged power spectrum i○
*Reported resolution corresponds to spatial frequency of 0.333 Å−1
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#raps
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8 Fourier-Shell correlation i○
This section was not generated. No FSC curve or half-maps provided.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validation
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9 Map-model fit i○
This section contains information regarding the fit between EMDB map EMD-21564 and PDBmodel 6W6V. Per-residue inclusion information can be found in section 3 on page 6.
9.1 Map-model overlay i○
X Y Z
The images above show the 3D surface view of the map at the recommended contour level 0.3 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 fit between the atomic model andthe map.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_fithttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_overlay
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9.2 Atom inclusion i○
At the recommended contour level, 93% of all backbone atoms, 90% of all non-hydrogen atoms,are inside the map.
https://www.wwpdb.org/validation/2017/EMValidationReportHelp#atom_inclusion_by_contour
Overall quality at a glanceEntry compositionResidue-property plotsExperimental informationModel qualityStandard geometryToo-close contactsTorsion anglesProtein backboneProtein sidechainsRNA
Non-standard residues in protein, DNA, RNA chainsCarbohydratesLigand geometryOther polymersPolymer linkage issues
Map visualisationOrthogonal projectionsPrimary map
Central slicesPrimary map
Largest variance slicesPrimary map
Orthogonal surface viewsPrimary map
Mask visualisation
Map analysisMap-value distributionVolume estimateRotationally averaged power spectrum
Fourier-Shell correlationMap-model fitMap-model overlayAtom inclusion