full wwpdb em map/model validation report o i · 2020. 5. 31. · full wwpdb em map/model...
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Full wwPDB EM Validation Report i○
Dec 13, 2020 – 05:07 PM EST
PDB ID : 6D6QEMDB ID : EMD-7808
Title : Human nuclear exosome-MTR4 RNA complex - overall reconstructionAuthors : Weick, E.-M.; Lima, C.D.
Deposited on : 2018-04-22Resolution : 3.45 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.dev61Mogul : 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) : 2.15.1
Page 2 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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 3.45 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 4297Ramachandran outliers 154571 4023
Sidechain 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 <=5%The upper red bar (where present) indicates the fraction of residues that have poor fit to the EMmap (all-atom inclusion < 40%). The numeric value is given above the bar.
Mol Chain Length Quality of chain
1 A 473
2 B 249
3 C 278
4 D 237
5 E 293
6 F 272
7 G 277Continued on next page...
Page 3 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Continued from previous page...Mol Chain Length Quality of chain
8 H 296
9 I 197
10 J 761
11 K 960
12 L 162
13 M 1045
14 N 16
15 O 62
Page 4 Full wwPDB EM Validation Report EMD-7808, 6D6Q
2 Entry composition i○
There are 18 unique types of molecules in this entry. The entry contains 31639 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 Exosome complex component RRP45.
Mol Chain Residues Atoms AltConf Trace
1 A 287 Total C N O S2264 1423 404 419 18 0 0
There are 17 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceA -16 MET - expression tag UNP Q06265A -15 GLY - expression tag UNP Q06265A -14 SER - expression tag UNP Q06265A -13 SER - expression tag UNP Q06265A -12 HIS - expression tag UNP Q06265A -11 HIS - expression tag UNP Q06265A -10 HIS - expression tag UNP Q06265A -9 HIS - expression tag UNP Q06265A -8 HIS - expression tag UNP Q06265A -7 HIS - expression tag UNP Q06265A -6 SER - expression tag UNP Q06265A -5 GLN - expression tag UNP Q06265A -4 ASP - expression tag UNP Q06265A -3 PRO - expression tag UNP Q06265A -2 ASN - expression tag UNP Q06265A -1 SER - expression tag UNP Q06265A 0 HIS - expression tag UNP Q06265
• Molecule 2 is a protein called Exosome complex component RRP41.
Mol Chain Residues Atoms AltConf Trace
2 B 241 Total C N O S1824 1126 345 344 9 0 0
There are 4 discrepancies between the modelled and reference sequences:
Page 5 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Chain Residue Modelled Actual Comment ReferenceB -4 MET - expression tag UNP Q9NPD3B -3 ALA - expression tag UNP Q9NPD3B -2 ASP - expression tag UNP Q9NPD3B -1 PRO - expression tag UNP Q9NPD3
• Molecule 3 is a protein called Exosome complex component RRP43.
Mol Chain Residues Atoms AltConf Trace
3 C 265 Total C N O S2020 1272 337 397 14 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceC -1 ASP - expression tag UNP Q96B26C 0 PRO - expression tag UNP Q96B26
• Molecule 4 is a protein called Exosome complex component RRP46.
Mol Chain Residues Atoms AltConf Trace
4 D 208 Total C N O S1566 979 278 297 12 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceD -1 SER - expression tag UNP Q9NQT4D 0 LEU - expression tag UNP Q9NQT4
• Molecule 5 is a protein called Exosome complex component RRP42.
Mol Chain Residues Atoms AltConf Trace
5 E 286 Total C N O S2194 1373 374 432 15 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceE -1 ASP - expression tag UNP Q15024E 0 PRO - expression tag UNP Q15024
• Molecule 6 is a protein called Exosome complex component MTR3.
Page 6 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Mol Chain Residues Atoms AltConf Trace
6 F 252 Total C N O S1859 1154 353 345 7 0 0
• Molecule 7 is a protein called Exosome complex component RRP40.
Mol Chain Residues Atoms AltConf Trace
7 G 237 Total C N O S1806 1136 329 329 12 0 0
There are 3 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceG -1 ASP - expression tag UNP Q9NQT5G 0 PRO - expression tag UNP Q9NQT5G 225 HIS TYR variant UNP Q9NQT5
• Molecule 8 is a protein called Exosome complex component RRP4.
Mol Chain Residues Atoms AltConf Trace
8 H 289 Total C N O S2263 1424 405 419 15 0 0
There are 3 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceH -2 ASP - expression tag UNP Q13868H -1 PRO - expression tag UNP Q13868H 0 HIS - expression tag UNP Q13868
• Molecule 9 is a protein called Exosome complex component CSL4.
Mol Chain Residues Atoms AltConf Trace
9 I 183 Total C N O S1407 884 247 266 10 0 0
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceI -1 ASP - expression tag UNP Q9Y3B2I 0 PRO - expression tag UNP Q9Y3B2
• Molecule 10 is a protein called Exosome component 10.
Page 7 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Mol Chain Residues Atoms AltConf Trace
10 J 11 Total C N O86 56 14 16 0 0
There are 14 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceJ 0 SER - expression tag UNP Q01780J 313 ASN ASP engineered mutation UNP Q01780J 649 SER - linker UNP Q01780J 650 ARG - linker UNP Q01780J 651 GLY - linker UNP Q01780J 652 SER - linker UNP Q01780J 653 GLY - linker UNP Q01780J 654 SER - linker UNP Q01780J 655 GLY - linker UNP Q01780J 656 SER - linker UNP Q01780J 657 GLY - linker UNP Q01780J 658 SER - linker UNP Q01780J 659 GLY - linker UNP Q01780J 660 SER - linker UNP Q01780
• Molecule 11 is a protein called Exosome complex exonuclease RRP44.
Mol Chain Residues Atoms AltConf Trace
11 K 853 Total C N O S6856 4329 1233 1260 34 0 0
There are 6 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceK -1 GLY - expression tag UNP Q9Y2L1K 0 SER - expression tag UNP Q9Y2L1K 146 ASN ASP engineered mutation UNP Q9Y2L1K 269 SER ASN variant UNP Q9Y2L1K 487 ASN ASP engineered mutation UNP Q9Y2L1K 843 ASN LYS variant UNP Q9Y2L1
• Molecule 12 is a protein called M-phase phosphoprotein 6.
Mol Chain Residues Atoms AltConf Trace
12 L 68 Total C N O S573 371 95 101 6 0 0
Page 8 Full wwPDB EM Validation Report EMD-7808, 6D6Q
There are 2 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceL -1 ASP - expression tag UNP Q99547L 0 PRO - expression tag UNP Q99547
• Molecule 13 is a protein called Exosome RNA helicase MTR4.
Mol Chain Residues Atoms AltConf Trace
13 M 709 Total C N O S5648 3589 963 1052 44 0 0
There are 3 discrepancies between the modelled and reference sequences:
Chain Residue Modelled Actual Comment ReferenceM -2 SER - expression tag UNP P42285M -1 GLY - expression tag UNP P42285M 0 ASP - expression tag UNP P42285
• Molecule 14 is a RNA chain called RNA (5’-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3’).
Mol Chain Residues Atoms AltConf Trace
14 N 13 Total C N O P278 126 56 84 12 0 0
• Molecule 15 is DNA/RNA hybrid called DNA/RNA (62-MER).
Mol Chain Residues Atoms AltConf Trace
15 O 48 Total C N O P966 443 172 304 47 0 0
• Molecule 16 is MAGNESIUM ION (three-letter code: MG) (formula: Mg).
Mol Chain Residues Atoms AltConf
16 K 1 Total Mg1 1 0
• Molecule 17 is ZINC ION (three-letter code: ZN) (formula: Zn).
Mol Chain Residues Atoms AltConf
17 K 1 Total Zn1 1 0
Page 9 Full wwPDB EM Validation Report EMD-7808, 6D6Q
• Molecule 18 is PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (three-letter code: ANP) (formula: C10H17N6O12P3).
Mol Chain Residues Atoms AltConf
18 M 1 Total C N O P27 10 6 9 2 0
Page 10 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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: Exosome complex component RRP45
Chain A:
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• Molecule 3: Exosome complex component RRP43
Chain C:
Page 11 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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• Molecule 4: Exosome complex component RRP46
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• Molecule 5: Exosome complex component RRP42
Chain E:
ASP
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T5 A9 E10
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• Molecule 6: Exosome complex component MTR3
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Page 12 Full wwPDB EM Validation Report EMD-7808, 6D6Q
• Molecule 7: Exosome complex component RRP40
Chain G:
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• Molecule 8: Exosome complex component RRP4
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• Molecule 9: Exosome complex component CSL4
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G161
�I1
62�
Q163
K176
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77H1
78�
T179
K180
�
R183
R187
�VA
LGL
N
PRO
GLU
PHE
LEU
GLN
THR
• Molecule 10: Exosome component 10
Chain J:
SER
MET
ALA
PRO
PRO
SER
THR
ARG
GLU
PRO
ARG
VAL
LEU
SER
ALA
THR
SER
ALA
THR
LYS
SER
ASP
GLY
GLU
MET
VAL
LEU
PRO
GLY
PHE
PRO
ASP
ALA
ASP
SER
PHE
VAL
LYS
PHE
ALA
LEU
GLY
SER
VAL
VAL
ALA
VAL
THR
LYS
ALA
SER
GLY
GLY
LEU
PRO
GLN
PHE
GLY
ASP
GLU
Page 13 Full wwPDB EM Validation Report EMD-7808, 6D6Q
TYR
ASP
PHE
TYR
ARG
SER
PHE
PRO
GLY
PHE
GLN
ALA
PHE
CYS
GLU
THR
GLN
GLY
ASP
ARG
LEU
LEU
GLN
CYS
MET
SER
ARG
VAL
MET
GLN
TYR
HIS
GLY
CYS
ARG
SER
ASN
ILE
LYS
ASP
ARG
SER
LYS
VAL
THR
GLU
LEU
GLU
ASP
LYS
PHE
ASP
LEU
LEU
VAL
ASP
ALA
ASN
ASP
VAL
ILE
LEU
GLU
ARG
VAL
GLY
ILE
LEU
LEU
ASP
GLU
ALA
SER
GLY
VAL
ASN
LYS
ASN
GLN
GLN
PRO
VAL
LEU
PRO
ALA
GLY
LEU
GLN
VAL
PRO
LYS
THR
VAL
VAL
SER
SER
TRP
ASN
ARG
LYS
ALA
ALA
GLU
TYR
GLY
LYS
LYS
ALA
LYS
SER
GLU
THR
PHE
ARG
LEU
LEU
HIS
ALA
LYS
ASN
ILE
ILE
ARG
PRO
GLN
LEU
LYS
PHE
ARG
GLU
LYS
ILE
ASP
ASN
SER
ASN
THR
PRO
PHE
LEU
PRO
LYS
ILE
PHE
ILE
LYS
PRO
ASN
ALA
GLN
LYS
PRO
LEU
PRO
GLN
ALA
LEU
SER
LYS
GLU
ARG
ARG
GLU
ARG
PRO
GLN
ASP
ARG
PRO
GLU
ASP
LEU
ASP
VAL
PRO
PRO
ALA
LEU
ALA
ASP
PHE
ILE
HIS
GLN
GLN
ARG
THR
GLN
GLN
VAL
GLU
GLN
ASP
MET
PHE
ALA
HIS
PRO
TYR
GLN
TYR
GLU
LEU
ASN
HIS
PHE
THR
PRO
ALA
ASP
ALA
VAL
LEU
GLN
LYS
PRO
GLN
PRO
GLN
LEU
TYR
ARG
PRO
ILE
GLU
GLU
THR
PRO
CYS
HIS
PHE
ILE
SER
SER
LEU
ASP
GLU
LEU
VAL
GLU
LEU
ASN
GLU
LYS
LEU
LEU
ASN
CYS
GLN
GLU
PHE
ALA
VAL
ASN
LEU
GLU
HIS
HIS
SER
TYR
ARG
SER
PHE
LEU
GLY
LEU
THR
CYS
LEU
MET
GLN
ILE
SER
THR
ARG
THR
GLU
ASP
PHE
ILE
ILE
ASP
THR
LEU
GLU
LEU
ARG
SER
ASP
MET
TYR
ILE
LEU
ASN
GLU
SER
LEU
THR
ASP
PRO
ALA
ILE
VAL
LYS
VAL
PHE
HIS
GLY
ALA
ASP
SER
ASP
ILE
GLU
TRP
LEU
GLN
LYS
ASP
PHE
GLY
LEU
TYR
VAL
VAL
ASN
MET
PHE
ASP
THR
HIS
GLN
ALA
ALA
ARG
LEU
LEU
ASN
LEU
GLY
ARG
HIS
SER
LEU
ASP
HIS
LEU
LEU
LYS
LEU
TYR
CYS
ASN
VAL
ASP
SER
ASN
LYS
GLN
TYR
GLN
LEU
ALA
ASP
TRP
ARG
ILE
ARG
PRO
LEU
PRO
GLU
GLU
MET
LEU
SER
TYR
ALA
ARG
ASP
ASP
THR
HIS
TYR
LEU
LEU
TYR
ILE
TYR
ASP
LYS
MET
ARG
LEU
GLU
MET
TRP
GLU
ARG
GLY
ASN
GLY
GLN
PRO
VAL
GLN
LEU
GLN
VAL
VAL
TRP
GLN
ARG
SER
ARG
ASP
ILE
CYS
LEU
LYS
LYS
PHE
ILE
LYS
PRO
ILE
PHE
THR
ASP
GLU
SER
TYR
LEU
GLU
LEU
TYR
ARG
LYS
GLN
LYS
LYS
HIS
LEU
ASN
THR
GLN
GLN
LEU
THR
ALA
PHE
GLN
LEU
LEU
PHE
ALA
TRP
ARG
ASP
LYS
THR
ALA
ARG
ARG
GLU
ASP
GLU
SER
TYR
GLY
TYR
VAL
LEU
PRO
ASN
HIS
MET
MET
LEU
LYS
ILE
ALA
GLU
GLU
LEU
PRO
LYS
GLU
PRO
GLN
GLY
ILE
ILE
ALA
CYS
CYS
ASN
PRO
VAL
PRO
PRO
LEU
VAL
ARG
GLN
GLN
ILE
ASN
GLU
MET
HIS
LEU
LEU
ILE
GLN
GLN
ALA
ARG
GLU
MET
PRO
LEU
LEU
LYS
SER
GLU
VAL
ALA
ALA
GLY
VAL
LYS
LYS
SER
GLY
PRO
LEU
PRO
SER
ALA
GLU
ARG
LEU
GLU
ASN
VAL
LEU
PHE
GLY
PRO
HIS
ASP
CYS
SER
HIS
ALA
PRO
PRO
ASP
GLY
TYR
PRO
ILE
ILE
PRO
THR
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GLY
SER
VAL
P630
V631
�
Q634
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37F6
38P6
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40�
GLU
LYS
GLU
ASP
ASN
LEU
LEU
GLY
SER
ARG
GLY
SER
GLY
SER
GLY
SER
GLY
SER
GLY
SER
VAL
SER
GLN
ALA
ALA
LYS
PHE
ASP
PRO
SER
THR
LYS
ILE
TYR
GLU
ILE
SER
ASN
ARG
TRP
LYS
LEU
ALA
GLN
VAL
GLN
VAL
GLN
LYS
ASP
SER
LYS
GLU
ALA
VAL
LYS
LYS
LYS
ALA
ALA
GLU
GLN
THR
ALA
ALA
ARG
GLU
GLN
ALA
LYS
GLU
ALA
CYS
LYS
ALA
ALA
ALA
GLU
GLN
ALA
ILE
SER
VAL
ARG
GLN
GLN
VAL
VAL
LEU
GLU
ASN
ALA
ALA
LYS
LYS
ARG
GLU
ARG
ALA
THR
SER
ASP
PRO
ARG
THR
THR
GLU
GLN
LYS
GLN
GLU
LYS
LYS
ARG
LEU
LYS
ILE
SER
LYS
LYS
• Molecule 11: Exosome complex exonuclease RRP44
Chain K:
GLY
SER
M1 T6 K9 I19
V20
R21
E22
R26
D27
D28
C36
�A3
7A3
8�
C39
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G41
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H43
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G45
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A47
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Q51
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RSE
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GLU
GLY
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LYS
I226
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GLU
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K273
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ASP
GLU
GLY
GLN
ASN
GLU
GLU
ASP
VAL
GLU
LYS
GLU
GLU
GLU
THR
GLU
ARG
MET
LEU
LYS
Page 14 Full wwPDB EM Validation Report EMD-7808, 6D6Q
THR
ALA
VAL
SER
GLU
LYS
MET
LEU
K340
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R344
V345
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R370
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T387
R388
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R397
I398
I399
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P406
R407
R410
Y411
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R418
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L420
E425
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E429
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PRO
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GLY
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ASP
THR
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MET
ASP
LEU
ASN
GLY
PRO
LYS
LYS
LYS
LYS
MET
LYS
LEU
GLY
LYS
• Molecule 12: M-phase phosphoprotein 6
Chain L:
ASP
PRO
MET
ALA
ALA
GLU
R5�
K6�
T7�
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S10
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GLU
THR
LYS
LYS
GLN
LEU
GLU
GLU
GLU
GLU
LYS
LYS
ILE
ILE
SER
GLU
GLU
H43
D47
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LGL
UAS
PGL
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RVA
LGL
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UAS
PVA
LSE
RAS
PGL
UGL
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GAR
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RGL
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RLE
UVA
LGL
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SLY
SPH
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GLY
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GAS
PHI
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AAS
NTY
RGL
UGL
UAS
P
GLU
ASN
GLY
ASP
ILE
THR
PRO
ILE
LYS
ALA
LYS
LYS
MET
PHE
LEU
LYS
PRO
GLN
ASP
• Molecule 13: Exosome RNA helicase MTR4
Chain M:
Page 15 Full wwPDB EM Validation Report EMD-7808, 6D6Q
SER
GLY
ASP
MET
ALA
ASP
ALA
PHE
GLY
ASP
GLU
LEU
PHE
SER
VAL
PHE
GLU
GLY
ASP
SER
THR
THR
ALA
ALA
GLY
THR
LYS
LYS
ASP
LYS
GLU
LYS
ASP
LYS
GLY
LYS
TRP
LYS
GLY
PRO
PRO
GLY
SER
ALA
ASP
LYS
ALA
GLY
LYS
ARG
PHE
ASP
GLY
LYS
LEU
GLN
SER
GLU
SER
THR
ASN
ASN
GLY
LYS
ASN
LYS
ARG
ASP
VAL
ASP
PHE
GLU
GLY
THR
ASP
GLU
PRO
ILE
PHE
GLY
LYS
LYS
PRO
ARG
ILE
GLU
GLU
SER
ILE
THR
GLU
ASP
LEU
SER
LEU
ALA
ASP
LEU
M96
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E105
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V107
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G109
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V114
A115
L116
P117
A118
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K126
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P127
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V129
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33K1
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E135
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I139
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D141
A142
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I148
Q149
C150
V151
S156
V157
L158
T163
S164
K167
T168
V169
C170
K182
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V185
I186
F187
T188
S189
P190
I191
K192
S195
R200
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E204
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06Q2
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D208
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V226
M227
E230
I231
L232
L236
Y237
M243
W248
V249
I250
F251
D252
�E2
53�
I254
H255
R258
E261
�R2
62
E267
E268
I271
L272
Y279
V280
F281
L282
R290
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• Molecule 14: RNA (5’-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3’)
Page 16 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Chain N:A1
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Page 17 Full wwPDB EM Validation Report EMD-7808, 6D6Q
4 Experimental information i○
Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, Not providedNumber of particles used 122703 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
) 85.23 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.154 DepositorMinimum map value -0.084 DepositorAverage map value 0.000 DepositorMap value standard deviation 0.003 DepositorRecommended contour level 0.025 DepositorMap size (Å) 410.88, 410.88, 410.88 wwPDBMap dimensions 384, 384, 384 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.07, 1.07, 1.07 Depositor
Page 18 Full wwPDB EM Validation Report EMD-7808, 6D6Q
5 Model quality i○
5.1 Standard geometry i○
Bond lengths and bond angles in the following residue types are not validated in this section: ZN,ANP, MG
The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).
Mol Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >5
1 A 0.39 0/2297 0.52 0/30942 B 0.41 0/1849 0.54 0/25003 C 0.38 0/2053 0.51 0/27864 D 0.39 0/1586 0.53 0/21455 E 0.40 0/2225 0.51 0/30076 F 0.37 0/1889 0.54 0/25627 G 0.34 0/1832 0.49 0/24678 H 0.40 0/2296 0.51 0/30929 I 0.30 0/1431 0.50 0/193210 J 0.26 0/88 0.47 0/11811 K 0.30 0/6991 0.49 1/9444 (0.0%)12 L 0.28 0/583 0.49 0/77613 M 0.31 0/5751 0.47 0/775214 N 0.22 0/312 0.76 0/48515 O 0.60 3/1077 (0.3%) 0.98 5/1668 (0.3%)All All 0.36 3/32260 (0.0%) 0.53 6/43828 (0.0%)
Chiral center outliers are detected by calculating the chiral volume of a chiral center and verifying ifthe center is modelled as a planar moiety or with the opposite hand.A planarity outlier is detectedby checking planarity of atoms in a peptide group, atoms in a mainchain group or atoms of asidechain that are expected to be planar.
Mol Chain #Chirality outliers #Planarity outliers2 B 0 111 K 0 1All All 0 2
All (3) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)15 O 17 C P-OP2 11.40 1.68 1.49
Continued on next page...
Page 19 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Continued from previous page...Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)15 O 16 DT O3’-P 8.20 1.71 1.6115 O 17 C P-OP1 6.26 1.59 1.49
All (6) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)15 O 16 DT O3’-P-O5’ 10.97 124.84 104.0011 K 648 PRO CA-N-CD -8.84 99.13 111.5015 O 16 DT P-O3’-C3’ -6.69 111.67 119.7015 O 16 DT OP2-P-O3’ -6.29 91.36 105.2015 O 17 C OP1-P-OP2 -5.92 110.72 119.6015 O 16 DT OP1-P-O3’ 5.73 117.81 105.20
There are no chirality outliers.
All (2) planarity outliers are listed below:
Mol Chain Res Type Group2 B 201 ASP Peptide11 K 455 MET Peptide
5.2 Too-close contacts i○
In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in the chain respectively. The H(added) column lists the number of 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 2264 0 2315 70 02 B 1824 0 1823 43 03 C 2020 0 2035 41 04 D 1566 0 1605 35 05 E 2194 0 2205 38 06 F 1859 0 1889 26 07 G 1806 0 1865 43 08 H 2263 0 2337 44 09 I 1407 0 1432 22 010 J 86 0 86 3 011 K 6856 0 6907 150 012 L 573 0 575 6 013 M 5648 0 5681 107 0
Continued on next page...
Page 20 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Continued from previous page...Mol Chain Non-H H(model) H(added) Clashes Symm-Clashes14 N 278 0 144 0 015 O 966 0 518 28 016 K 1 0 0 0 017 K 1 0 0 0 018 M 27 0 12 2 0All All 31639 0 31429 601 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 10.
All (601) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
13:M:237:TYR:OH 13:M:268:GLU:OE2 1.78 0.9911:K:780:ARG:NH2 15:O:61:A:OP2 1.97 0.973:C:111:ASP:OD1 3:C:115:ASN:ND2 1.97 0.9615:O:42:C:O2’ 15:O:43:A:O5’ 1.82 0.95
11:K:565:GLU:OE1 11:K:574:LYS:NZ 2.05 0.8811:K:780:ARG:NH1 15:O:62:A:OP2 2.08 0.86
2:B:7:SER:OG 2:B:9:GLN:OE1 1.92 0.862:B:108:ALA:O 2:B:153:ARG:NH1 2.11 0.842:B:182:PRO:HA 2:B:202:ALA:HB3 1.60 0.84
13:M:267:GLU:OE2 13:M:561:SER:OG 1.96 0.8311:K:467:ARG:NH2 11:K:508:ASP:OD2 2.11 0.832:B:22:ARG:NE 2:B:171:ASP:OD2 2.10 0.83
13:M:189:SER:OG 13:M:195:SER:OG 1.96 0.8113:M:393:SER:OG 13:M:399:CYS:SG 2.38 0.8111:K:884:GLN:NE2 11:K:897:GLU:OE2 2.13 0.8011:K:709:ARG:NH2 11:K:903:VAL:O 2.15 0.8011:K:753:TYR:HH 11:K:774:HIS:HD1 1.26 0.805:E:39:THR:OG1 5:E:162:ASN:OD1 1.98 0.807:G:17:ALA:N 7:G:33:GLU:O 2.15 0.79
1:A:144:ASN:ND2 1:A:147:ASP:OD2 2.15 0.795:E:175:GLU:OE2 11:K:285:ARG:NH1 2.16 0.7811:K:135:GLN:NE2 11:K:139:GLU:O 2.16 0.7811:K:130:GLU:OE1 11:K:155:TRP:NE1 2.17 0.7813:M:267:GLU:O 13:M:271:ILE:HD12 1.84 0.789:I:158:SER:N 9:I:162:ILE:O 2.18 0.767:G:188:ASN:O 12:L:72:TYR:OH 2.04 0.76
1:A:245:ASP:OD2 1:A:249:ARG:NH2 2.20 0.755:E:73:LYS:NZ 5:E:76:GLU:OE2 2.19 0.74
Continued on next page...
Page 21 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
13:M:156:SER:OG 13:M:279:TYR:O 2.02 0.7411:K:47:ALA:O 11:K:119:HIS:ND1 2.21 0.73
13:M:560:ASN:OD1 13:M:593:GLN:NE2 2.23 0.7211:K:753:TYR:OH 11:K:774:HIS:ND1 2.19 0.7211:K:624:ARG:NH1 11:K:665:GLU:OE2 2.23 0.7213:M:995:ARG:NH1 15:O:20:C:OP2 2.22 0.7213:M:903:GLU:O 13:M:906:THR:OG1 2.04 0.7211:K:411:TYR:OH 15:O:51:A:OP1 2.05 0.7211:K:229:SER:OG 11:K:284:ASN:OD1 2.08 0.7011:K:738:THR:O 11:K:742:ILE:HD12 1.91 0.708:H:235:SER:OG 8:H:268:ILE:HD11 1.91 0.703:C:25:ASP:OD2 3:C:27:ARG:NE 2.26 0.69
13:M:252:ASP:OD1 13:M:282:LEU:HD12 1.93 0.6913:M:569:MET:O 13:M:573:LEU:HD23 1.93 0.698:H:143:ALA:HB3 8:H:156:LEU:HD12 1.75 0.691:A:35:ILE:HD11 1:A:264:LEU:HD23 1.73 0.693:C:89:CYS:SG 3:C:90:SER:N 2.66 0.68
11:K:675:ALA:HB2 11:K:773:THR:HG22 1.74 0.6811:K:181:LYS:O 11:K:185:ILE:HD12 1.94 0.6815:O:42:C:HO2’ 15:O:43:A:P 2.16 0.672:B:228:ASP:OD1 2:B:229:ARG:N 2.28 0.679:I:60:GLU:OE2 9:I:96:LYS:NZ 2.28 0.6713:M:163:THR:O 13:M:164:SER:OG 2.08 0.6711:K:487:ASN:OD1 11:K:488:ASP:N 2.28 0.6711:K:552:LYS:O 11:K:584:SER:OG 2.12 0.66
7:G:164:TYR:HB2 7:G:193:ILE:HD11 1.76 0.6611:K:922:LYS:NZ 15:O:53:A:O2’ 2.28 0.6611:K:442:GLN:O 11:K:526:ARG:NH2 2.29 0.664:D:62:ALA:O 4:D:114:THR:OG1 2.11 0.66
11:K:410:ARG:NH2 15:O:50:C:O3’ 2.30 0.6511:K:89:ILE:HD13 11:K:156:TYR:CE2 2.31 0.6513:M:465:GLU:OE1 13:M:1040:LEU:N 2.28 0.651:A:32:TYR:OH 1:A:194:VAL:HG13 1.97 0.65
3:C:168:VAL:HG12 3:C:179:VAL:HG12 1.77 0.6511:K:139:GLU:OE1 11:K:147:ARG:NH1 2.30 0.6513:M:230:GLU:OE1 15:O:21:A:O2’ 2.13 0.6511:K:21:ARG:NH2 15:O:45:C:N3 2.41 0.6511:K:837:GLN:NE2 11:K:921:GLN:O 2.29 0.641:A:35:ILE:HD11 1:A:264:LEU:CD2 2.26 0.641:A:241:MET:CE 2:B:108:ALA:HB1 2.28 0.64
11:K:397:ARG:HD3 11:K:432:VAL:HG21 1.79 0.63Continued on next page...
Page 22 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
5:E:199:CYS:SG 5:E:267:HIS:NE2 2.72 0.6311:K:295:GLU:OE1 11:K:344:ARG:NH2 2.31 0.6311:K:208:ILE:O 11:K:212:ALA:N 2.30 0.63
6:F:219:LEU:HD23 6:F:219:LEU:H 1.64 0.638:H:240:CYS:O 8:H:243:SER:OG 2.16 0.62
13:M:250:ILE:HG22 13:M:280:VAL:HB 1.81 0.6213:M:590:TYR:O 13:M:594:HIS:ND1 2.33 0.62
13:M:482:THR:HG23 13:M:483:GLU:H 1.65 0.6211:K:380:ILE:O 15:O:51:A:N6 2.33 0.62
2:B:156:VAL:HG13 2:B:156:VAL:O 1.99 0.618:H:28:VAL:N 8:H:31:ASP:OD2 2.31 0.61
6:F:40:TYR:CE2 10:J:635:ALA:HB2 2.35 0.614:D:47:PHE:HD2 4:D:132:CYS:HG 1.48 0.612:B:44:ASN:ND2 11:K:22:GLU:OE2 2.33 0.6111:K:89:ILE:HD13 11:K:156:TYR:CZ 2.35 0.616:F:108:ARG:NH2 6:F:205:GLU:OE2 2.33 0.615:E:161:PHE:O 5:E:191:ARG:NH2 2.32 0.61
11:K:898:ASP:OD1 11:K:899:THR:N 2.34 0.6111:K:397:ARG:NE 11:K:429:GLU:OE2 2.33 0.601:A:225:MET:SD 1:A:231:ILE:HD13 2.41 0.6011:K:505:HIS:CE1 11:K:561:SER:HG 2.18 0.602:B:35:ASP:OD2 8:H:75:ARG:NH1 2.34 0.603:C:22:CYS:SG 3:C:23:ARG:N 2.75 0.6011:K:570:ALA:O 11:K:623:ARG:NH1 2.35 0.608:H:33:ILE:HG21 8:H:67:ILE:HG21 1.84 0.591:A:76:LEU:HD12 1:A:116:ILE:HD11 1.84 0.592:B:182:PRO:CA 2:B:202:ALA:HB3 2.32 0.594:D:80:LEU:HD22 4:D:91:GLU:OE1 2.03 0.5911:K:567:ASN:ND2 11:K:571:GLU:OE2 2.33 0.59
1:A:52:LYS:O 1:A:140:ASN:ND2 2.36 0.5913:M:1016:ASN:OD1 13:M:1017:THR:N 2.36 0.5813:M:407:THR:O 13:M:450:ARG:NH1 2.36 0.5811:K:26:ARG:NH2 11:K:28:ASP:OD2 2.35 0.585:E:23:ARG:O 5:E:26:GLY:N 2.33 0.586:F:183:CYS:SG 6:F:197:LEU:HD11 2.44 0.584:D:184:ALA:HB3 4:D:194:MET:HB3 1.86 0.589:I:70:ILE:HG23 9:I:70:ILE:O 2.04 0.588:H:121:ARG:HG2 8:H:122:ARG:N 2.19 0.575:E:225:SER:OG 5:E:242:VAL:HG13 2.05 0.573:C:29:LEU:HD23 3:C:29:LEU:O 2.04 0.5711:K:615:LYS:O 11:K:619:ILE:HD12 2.05 0.57
Continued on next page...
Page 23 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:244:LYS:O 1:A:247:VAL:HG22 2.04 0.572:B:42:GLN:NE2 2:B:171:ASP:OD1 2.38 0.575:E:199:CYS:HG 5:E:267:HIS:CD2 2.22 0.572:B:159:CYS:SG 2:B:160:SER:N 2.78 0.577:G:36:LEU:H 7:G:36:LEU:HD23 1.70 0.57
11:K:477:SER:OG 11:K:486:ILE:HD11 2.04 0.5711:K:886:ILE:HB 11:K:895:LYS:HB2 1.86 0.56
13:M:381:ILE:HG23 13:M:386:PHE:HB2 1.87 0.5613:M:482:THR:HG23 13:M:483:GLU:N 2.21 0.5611:K:369:ARG:O 11:K:371:HIS:ND1 2.39 0.564:D:102:CYS:O 4:D:106:VAL:HG12 2.06 0.56
11:K:6:THR:HG22 11:K:20:VAL:HG22 1.88 0.564:D:54:VAL:HG12 4:D:132:CYS:SG 2.46 0.5611:K:798:ASP:OD1 11:K:799:CYS:N 2.37 0.561:A:25:ASP:OD2 1:A:27:ARG:NH1 2.39 0.56
11:K:125:ASN:OD1 11:K:126:GLU:N 2.39 0.562:B:186:LEU:CD2 2:B:216:ALA:HB1 2.36 0.554:D:186:ASP:OD1 4:D:187:SER:N 2.37 0.551:A:241:MET:HE3 2:B:108:ALA:HB1 1.87 0.557:G:182:ASP:OD1 7:G:183:SER:N 2.37 0.552:B:154:ASP:OD1 2:B:155:PHE:N 2.39 0.558:H:76:TYR:N 8:H:101:ASN:O 2.36 0.558:H:271:ILE:O 8:H:271:ILE:HD12 2.07 0.553:C:33:ARG:NE 3:C:209:ASP:OD2 2.40 0.559:I:79:ASN:OD1 9:I:80:SER:N 2.38 0.55
11:K:419:ASN:OD1 11:K:420:LEU:N 2.39 0.558:H:79:GLU:O 8:H:145:VAL:HG11 2.07 0.555:E:185:ASP:O 5:E:188:ASP:N 2.39 0.55
13:M:186:ILE:HD11 13:M:227:MET:HE3 1.89 0.5511:K:177:ASP:OD2 11:K:179:ARG:NH2 2.40 0.5411:K:711:LEU:HD12 11:K:728:ALA:HA 1.89 0.5413:M:479:LEU:HD21 13:M:485:PHE:CZ 2.42 0.548:H:63:VAL:HG12 8:H:64:ASN:H 1.71 0.5411:K:257:ASN:OD1 11:K:258:TYR:N 2.40 0.542:B:92:ASP:OD1 2:B:93:ARG:N 2.38 0.541:A:192:ILE:HD11 1:A:258:VAL:HG22 1.87 0.546:F:171:ASP:OD1 6:F:266:ARG:NH2 2.32 0.54
13:M:114:VAL:HG12 13:M:305:HIS:ND1 2.23 0.547:G:169:VAL:O 7:G:169:VAL:HG23 2.08 0.54
8:H:115:LEU:HD21 8:H:123:ARG:CZ 2.38 0.5411:K:51:GLN:HG2 11:K:51:GLN:O 2.08 0.54
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Page 24 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
11:K:774:HIS:NE2 15:O:60:A:OP1 2.41 0.5413:M:297:CYS:O 13:M:301:LYS:N 2.40 0.541:A:219:GLY:HA3 1:A:240:ILE:HG21 1.90 0.5412:L:48:LEU:O 12:L:52:LYS:N 2.41 0.5413:M:167:LYS:N 18:M:2001:ANP:O1B 2.41 0.541:A:75:ILE:HG22 1:A:76:LEU:N 2.23 0.5313:M:850:GLU:O 13:M:854:ARG:HG2 2.08 0.533:C:227:ASP:OD1 3:C:228:GLU:N 2.37 0.5313:M:972:THR:O 13:M:975:THR:OG1 2.24 0.531:A:19:GLU:OE2 1:A:200:GLN:NE2 2.40 0.535:E:45:THR:HG1 5:E:48:SER:HG 1.54 0.5311:K:246:TYR:CE1 11:K:346:VAL:HG21 2.44 0.538:H:266:HIS:ND1 8:H:276:ILE:HG23 2.23 0.53
11:K:112:VAL:HG11 11:K:120:PHE:CE2 2.43 0.533:C:217:LEU:O 3:C:217:LEU:HD12 2.09 0.53
13:M:314:THR:HG21 13:M:525:GLY:HA2 1.89 0.5313:M:168:THR:HG22 13:M:168:THR:O 2.09 0.5313:M:414:ASP:OD1 13:M:415:GLU:N 2.42 0.53
5:E:105:ILE:O 5:E:108:THR:OG1 2.23 0.521:A:164:ASP:OD1 1:A:165:VAL:N 2.42 0.527:G:90:GLU:N 7:G:90:GLU:OE1 2.42 0.527:G:189:GLY:O 12:L:74:ARG:NH1 2.42 0.52
11:K:536:ARG:NH1 11:K:538:ASP:OD1 2.42 0.525:E:45:THR:OG1 5:E:48:SER:OG 2.26 0.522:B:163:PHE:HB3 2:B:182:PRO:HG2 1.92 0.525:E:162:ASN:ND2 5:E:162:ASN:O 2.43 0.5211:K:493:ARG:NH2 11:K:501:GLU:OE1 2.43 0.5213:M:954:ASP:OD1 13:M:955:GLU:N 2.43 0.52
1:A:145:ILE:O 1:A:148:ALA:N 2.42 0.528:H:170:VAL:HG22 8:H:171:LEU:H 1.74 0.5211:K:177:ASP:OD1 11:K:180:ASN:ND2 2.42 0.527:G:18:ARG:HH12 7:G:23:VAL:HG11 1.75 0.528:H:170:VAL:HG22 8:H:171:LEU:N 2.25 0.5213:M:546:THR:HG23 13:M:547:ILE:N 2.25 0.52
5:E:276:LYS:O 5:E:279:SER:OG 2.15 0.513:C:77:GLY:HA2 3:C:132:VAL:HG22 1.92 0.5113:M:973:TRP:O 13:M:1032:ARG:NH2 2.44 0.511:A:86:ALA:HB3 1:A:90:PHE:HD2 1.76 0.517:G:23:VAL:HG12 7:G:26:GLN:OE1 2.10 0.517:G:66:VAL:HG13 7:G:99:VAL:HG23 1.92 0.5111:K:382:ARG:NE 15:O:51:A:O4’ 2.44 0.51
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Page 25 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
3:C:145:ASP:O 3:C:212:GLY:N 2.44 0.511:A:108:ARG:HD2 2:B:201:ASP:HB3 1.93 0.514:D:58:VAL:HG23 4:D:140:ALA:HB1 1.92 0.505:E:287:VAL:O 5:E:287:VAL:HG13 2.10 0.50
8:H:120:LEU:HD12 8:H:120:LEU:O 2.11 0.5013:M:391:ILE:HG23 13:M:497:LEU:HD11 1.93 0.504:D:79:ILE:HD11 4:D:119:VAL:HG13 1.93 0.506:F:177:TYR:O 9:I:27:TYR:OH 2.19 0.50
11:K:688:LEU:HD23 11:K:771:ILE:HG23 1.92 0.5011:K:228:PHE:O 11:K:407:ARG:NE 2.44 0.50
13:M:551:LEU:HD22 13:M:552:LEU:HD12 1.93 0.5015:O:59:A:H2’ 15:O:60:A:C8 2.45 0.50
1:A:225:MET:HB2 1:A:258:VAL:HG21 1.93 0.502:B:200:MET:CE 2:B:204:LEU:HD21 2.41 0.503:C:125:CYS:HA 3:C:132:VAL:HG23 1.93 0.504:D:131:ALA:O 4:D:135:ASN:ND2 2.45 0.509:I:130:ALA:HA 9:I:151:LEU:HD12 1.94 0.504:D:153:CYS:SG 4:D:220:VAL:HG11 2.52 0.5013:M:1039:SER:O 13:M:1042:LEU:N 2.43 0.5015:O:45:C:OP2 15:O:46:A:N6 2.45 0.501:A:25:ASP:OD1 1:A:26:GLY:N 2.44 0.508:H:80:VAL:HG12 8:H:80:VAL:O 2.12 0.504:D:153:CYS:SG 4:D:154:GLY:N 2.85 0.497:G:163:ILE:HG22 7:G:164:TYR:N 2.26 0.491:A:59:VAL:HG23 1:A:156:ALA:HB1 1.94 0.494:D:53:SER:N 4:D:124:SER:OG 2.46 0.49
11:K:399:ILE:HG13 11:K:417:VAL:CG2 2.43 0.4913:M:861:LEU:O 13:M:873:LYS:NZ 2.44 0.492:B:225:THR:O 2:B:228:ASP:OD1 2.30 0.494:D:141:LEU:O 4:D:146:VAL:HG12 2.13 0.498:H:64:ASN:OD1 13:M:873:LYS:NZ 2.34 0.4913:M:232:LEU:O 13:M:236:LEU:HD23 2.13 0.49
6:F:200:THR:HG22 6:F:201:ARG:N 2.28 0.4911:K:182:GLU:O 11:K:186:GLU:OE1 2.31 0.49
11:K:923:ILE:HG22 11:K:924:ARG:N 2.28 0.4913:M:186:ILE:HD11 13:M:227:MET:CE 2.42 0.4913:M:331:VAL:HG23 13:M:332:VAL:N 2.28 0.49
13:M:598:ILE:N 13:M:599:PRO:CD 2.76 0.492:B:186:LEU:HD22 2:B:216:ALA:HB1 1.95 0.495:E:33:ARG:HE 5:E:53:LEU:HD21 1.77 0.49
11:K:227:ILE:HG23 11:K:227:ILE:O 2.12 0.49Continued on next page...
Page 26 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:14:LEU:O 1:A:18:ILE:HG12 2.12 0.491:A:199:PHE:CE2 1:A:206:LEU:HD13 2.48 0.493:C:204:THR:O 3:C:247:LYS:NZ 2.42 0.495:E:27:ARG:NH2 5:E:213:ASP:OD2 2.37 0.487:G:132:ASP:OD1 7:G:133:VAL:N 2.47 0.488:H:41:ARG:NH2 8:H:45:THR:O 2.40 0.4811:K:284:ASN:O 11:K:285:ARG:HG2 2.12 0.488:H:33:ILE:HG22 8:H:34:THR:N 2.28 0.4813:M:907:ALA:O 13:M:910:SER:OG 2.23 0.4811:K:428:THR:O 11:K:432:VAL:HG23 2.13 0.4815:O:42:C:H2’ 15:O:43:A:O4’ 2.13 0.482:B:222:ASP:O 2:B:225:THR:OG1 2.22 0.48
1:A:12:ARG:NH1 7:G:195:GLN:OE1 2.46 0.481:A:49:GLU:HB3 1:A:54:ARG:HG2 1.94 0.48
13:M:185:VAL:HG22 13:M:186:ILE:N 2.29 0.4813:M:928:LEU:HD21 13:M:967:MET:HB3 1.95 0.481:A:146:ILE:HD12 1:A:146:ILE:H 1.78 0.481:A:199:PHE:CD2 1:A:206:LEU:HD13 2.49 0.485:E:25:ASP:OD1 8:H:238:ARG:NH1 2.46 0.48
13:M:163:THR:HG22 13:M:164:SER:N 2.28 0.4813:M:438:LEU:HD12 13:M:439:PRO:HD2 1.95 0.4813:M:576:VAL:HG12 13:M:577:GLU:N 2.28 0.483:C:232:LEU:HD11 3:C:252:MET:HE3 1.95 0.4811:K:889:ASP:OD1 11:K:890:GLU:N 2.46 0.4813:M:168:THR:OG1 18:M:2001:ANP:O2B 2.12 0.4813:M:840:LYS:O 13:M:844:THR:HG21 2.13 0.48
11:K:287:VAL:HG12 11:K:288:HIS:N 2.29 0.481:A:76:LEU:CD1 1:A:116:ILE:HD11 2.44 0.484:D:232:TYR:OH 7:G:83:CYS:SG 2.32 0.481:A:49:GLU:OE1 1:A:54:ARG:NH1 2.46 0.472:B:51:VAL:O 2:B:51:VAL:HG23 2.14 0.474:D:33:CYS:SG 4:D:34:GLU:N 2.87 0.475:E:199:CYS:HG 5:E:267:HIS:HE2 1.52 0.475:E:35:VAL:HG13 5:E:35:VAL:O 2.14 0.471:A:239:GLY:N 2:B:104:GLN:OE1 2.43 0.473:C:82:ASN:OD1 3:C:138:ASP:HA 2.14 0.473:C:148:ILE:HG13 3:C:152:CYS:HG 1.78 0.4711:K:735:TYR:O 11:K:739:LEU:HD13 2.15 0.472:B:3:LEU:O 11:K:99:ARG:NH2 2.47 0.47
13:M:576:VAL:HG11 13:M:579:ILE:HG22 1.95 0.4711:K:407:ARG:O 11:K:407:ARG:HG2 2.15 0.47
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Page 27 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
12:L:83:GLU:O 12:L:86:LYS:HG2 2.14 0.4713:M:479:LEU:HD21 13:M:485:PHE:CE2 2.49 0.476:F:178:ASP:OD1 6:F:179:LEU:N 2.45 0.478:H:63:VAL:HG12 8:H:64:ASN:N 2.29 0.479:I:148:GLU:HB3 9:I:151:LEU:HD23 1.95 0.471:A:13:PHE:CE2 7:G:248:LEU:HD21 2.50 0.47
3:C:134:VAL:HG13 3:C:134:VAL:O 2.14 0.479:I:105:LYS:HE2 9:I:116:VAL:HG23 1.95 0.47
11:K:913:LEU:HD23 11:K:913:LEU:H 1.79 0.471:A:241:MET:HB3 2:B:194:GLN:HB3 1.97 0.478:H:154:VAL:O 8:H:154:VAL:HG13 2.14 0.47
13:M:151:VAL:HG21 13:M:170:CYS:SG 2.55 0.479:I:145:THR:HG22 9:I:147:ALA:H 1.80 0.4711:K:106:TYR:CZ 11:K:110:ARG:HD2 2.50 0.47
13:M:389:VAL:HG23 13:M:495:THR:HG23 1.95 0.4713:M:579:ILE:HD11 13:M:583:TYR:CD2 2.49 0.473:C:32:PHE:HE1 3:C:208:VAL:HB 1.79 0.475:E:78:TYR:CE1 5:E:134:VAL:HG12 2.50 0.47
7:G:112:VAL:HG12 7:G:113:LYS:N 2.30 0.4711:K:87:ASN:OD1 11:K:88:VAL:N 2.48 0.4711:K:617:ALA:HB1 11:K:662:MET:HA 1.97 0.4711:K:873:VAL:O 11:K:873:VAL:HG13 2.15 0.47
3:C:194:VAL:HG21 3:C:262:VAL:CG2 2.44 0.473:C:62:VAL:HG13 3:C:62:VAL:O 2.14 0.477:G:162:LEU:HD23 7:G:162:LEU:H 1.80 0.478:H:115:LEU:HD21 8:H:123:ARG:NH1 2.30 0.471:A:121:LEU:O 1:A:121:LEU:HD12 2.15 0.46
3:C:50:LEU:HD22 10:J:637:LEU:CD1 2.45 0.466:F:31:ARG:NH2 6:F:196:LEU:HB3 2.30 0.467:G:207:ILE:HD13 7:G:232:GLY:O 2.14 0.4611:K:509:VAL:CG1 11:K:513:ILE:HD12 2.45 0.4613:M:581:PRO:O 13:M:584:MET:N 2.48 0.463:C:161:LYS:HG2 3:C:189:ILE:HD11 1.97 0.465:E:9:ALA:HB1 8:H:168:GLN:HB3 1.98 0.46
13:M:333:ASP:OD1 13:M:334:GLU:N 2.45 0.462:B:5:LEU:HD22 2:B:176:GLU:HB3 1.97 0.463:C:145:ASP:OD1 3:C:211:THR:OG1 2.33 0.467:G:22:THR:HG22 7:G:22:THR:O 2.16 0.469:I:154:VAL:HG23 9:I:155:VAL:N 2.31 0.4611:K:569:ASN:ND2 11:K:569:ASN:O 2.46 0.4613:M:150:CYS:SG 13:M:305:HIS:CD2 3.08 0.46
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Page 28 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
13:M:508:ASP:OD1 13:M:509:PHE:N 2.49 0.463:C:221:THR:HG22 3:C:222:LEU:N 2.29 0.467:G:221:VAL:HG12 7:G:227:LEU:HD21 1.98 0.468:H:72:LEU:HD23 8:H:72:LEU:H 1.79 0.4613:M:936:GLN:O 13:M:940:LYS:HG3 2.15 0.466:F:113:PRO:N 6:F:114:PRO:CD 2.79 0.461:A:98:LEU:O 1:A:102:LEU:HD13 2.16 0.46
11:K:595:LEU:O 11:K:599:SER:CB 2.64 0.4611:K:716:ASP:OD1 11:K:717:THR:N 2.48 0.4613:M:116:LEU:HD12 13:M:117:PRO:O 2.15 0.461:A:59:VAL:CG2 1:A:156:ALA:HB1 2.46 0.46
13:M:314:THR:HG21 13:M:525:GLY:CA 2.45 0.466:F:120:ARG:O 6:F:124:LEU:HD23 2.16 0.46
11:K:128:HIS:HB3 11:K:131:THR:HG22 1.98 0.4611:K:88:VAL:CG1 11:K:120:PHE:CD1 2.99 0.461:A:35:ILE:HG22 1:A:50:LEU:CB 2.46 0.4611:K:240:GLY:HA2 11:K:243:SER:HG 1.81 0.4611:K:283:LEU:O 11:K:285:ARG:N 2.49 0.462:B:73:CYS:SG 2:B:103:ARG:HB2 2.56 0.45
9:I:128:VAL:HG12 9:I:153:VAL:HA 1.97 0.4511:K:649:ILE:H 11:K:649:ILE:HD12 1.81 0.45
11:K:735:TYR:CE2 11:K:739:LEU:HD11 2.51 0.453:C:33:ARG:CD 3:C:209:ASP:OD2 2.65 0.451:A:35:ILE:HG22 1:A:50:LEU:HB2 1.97 0.453:C:234:CYS:HA 4:D:197:THR:CG2 2.46 0.455:E:201:VAL:HG12 5:E:203:LEU:CD1 2.47 0.456:F:66:VAL:HG23 6:F:168:ALA:HB1 1.98 0.4513:M:512:ILE:CG2 13:M:551:LEU:HD11 2.46 0.453:C:82:ASN:OD1 3:C:82:ASN:O 2.34 0.4511:K:859:ALA:HA 11:K:873:VAL:O 2.16 0.4511:K:9:LYS:HD2 15:O:45:C:O4’ 2.16 0.4513:M:394:PHE:CZ 13:M:512:ILE:HD13 2.52 0.452:B:54:PRO:HA 2:B:119:GLN:O 2.17 0.452:B:54:PRO:O 8:H:103:ARG:HA 2.15 0.45
13:M:187:PHE:HD1 13:M:250:ILE:CD1 2.29 0.457:G:161:ASP:OD1 7:G:162:LEU:N 2.50 0.4511:K:255:ARG:HG2 11:K:379:ARG:HE 1.82 0.4513:M:144:GLN:O 13:M:148:ILE:HG12 2.17 0.451:A:63:LEU:HD11 1:A:130:TRP:CZ3 2.52 0.4511:K:895:LYS:HG2 11:K:900:VAL:HG12 1.97 0.454:D:157:CYS:SG 4:D:181:LEU:HB2 2.57 0.45
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Page 29 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:241:VAL:O 6:F:245:LEU:HD13 2.17 0.4511:K:589:THR:O 11:K:593:ALA:N 2.44 0.451:A:27:ARG:NH2 1:A:208:ASP:O 2.50 0.443:C:161:LYS:CG 3:C:189:ILE:HD11 2.48 0.44
11:K:88:VAL:HG12 11:K:120:PHE:CD1 2.53 0.4413:M:498:PHE:HB2 13:M:537:LEU:HD12 1.98 0.444:D:135:ASN:OD1 4:D:224:TYR:OH 2.35 0.445:E:200:ILE:HG22 5:E:201:VAL:N 2.33 0.448:H:142:SER:N 8:H:166:LEU:HD11 2.33 0.448:H:179:VAL:O 8:H:179:VAL:HG23 2.17 0.44
11:K:597:ILE:HG12 11:K:610:LEU:HB3 2.00 0.4411:K:663:VAL:O 11:K:667:MET:HG2 2.17 0.4413:M:249:VAL:O 13:M:279:TYR:HB2 2.18 0.4415:O:61:A:H2’ 15:O:62:A:C5’ 2.48 0.443:C:200:VAL:O 3:C:200:VAL:HG13 2.17 0.44
11:K:383:ILE:HG22 11:K:384:ARG:N 2.31 0.4413:M:258:ARG:NH1 13:M:558:PRO:O 2.44 0.44
7:G:217:ILE:O 7:G:221:VAL:HG23 2.18 0.4413:M:871:GLU:O 13:M:874:GLY:N 2.47 0.441:A:53:THR:OG1 1:A:142:ASP:O 2.36 0.4411:K:564:TRP:CD1 11:K:575:THR:HG22 2.53 0.4413:M:576:VAL:CG1 13:M:579:ILE:HG22 2.47 0.442:B:217:ALA:O 2:B:221:ARG:HD3 2.17 0.445:E:56:THR:O 5:E:56:THR:HG23 2.18 0.449:I:179:THR:O 9:I:179:THR:HG23 2.17 0.44
13:M:331:VAL:HG21 13:M:552:LEU:CD2 2.46 0.441:A:219:GLY:HA3 1:A:240:ILE:HG12 1.99 0.444:D:71:PHE:O 4:D:72:ASN:OD1 2.36 0.44
5:E:173:ASP:OD1 5:E:174:GLU:N 2.48 0.4411:K:382:ARG:HB2 11:K:411:TYR:CE1 2.53 0.4411:K:874:PHE:HE2 15:O:53:A:HO2’ 1.64 0.4413:M:255:HIS:NE2 13:M:487:MET:SD 2.90 0.44
5:E:11:LYS:O 5:E:15:VAL:HG13 2.18 0.448:H:271:ILE:HG22 8:H:276:ILE:HG21 1.99 0.449:I:104:ARG:HE 9:I:143:LEU:HD23 1.83 0.4411:K:37:ALA:O 11:K:38:ALA:HB3 2.17 0.4413:M:457:GLY:N 15:O:19:C:OP1 2.46 0.444:D:37:LEU:HD11 4:D:46:SER:HB2 2.00 0.447:G:147:GLU:HB2 7:G:187:ALA:HB2 2.00 0.4411:K:662:MET:SD 11:K:663:VAL:N 2.91 0.4413:M:231:ILE:HD12 15:O:23:A:O4’ 2.18 0.44
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Page 30 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
1:A:153:ALA:O 1:A:157:LEU:HD13 2.17 0.437:G:129:PHE:CE2 7:G:141:LEU:HD12 2.52 0.4311:K:365:ILE:HD12 11:K:365:ILE:H 1.83 0.4311:K:357:CYS:SG 11:K:399:ILE:HG22 2.58 0.432:B:57:ILE:HG22 2:B:119:GLN:HG3 1.99 0.436:F:187:LEU:HD22 6:F:208:ALA:HB3 1.99 0.4311:K:171:VAL:HG22 11:K:172:ILE:N 2.33 0.4311:K:459:ILE:HG23 11:K:459:ILE:O 2.18 0.431:A:82:LEU:HD12 1:A:99:LEU:CD1 2.48 0.4313:M:394:PHE:HA 13:M:482:THR:HG1 1.82 0.43
15:O:42:C:C2’ 15:O:43:A:O5’ 2.64 0.431:A:106:MET:HE3 1:A:153:ALA:HB2 2.00 0.431:A:219:GLY:CA 1:A:240:ILE:HG21 2.48 0.435:E:53:LEU:O 5:E:56:THR:HG22 2.19 0.43
11:K:668:LEU:HD22 11:K:767:LEU:HD21 2.00 0.4311:K:285:ARG:HB3 11:K:405:TRP:CD1 2.54 0.4311:K:397:ARG:NH1 11:K:919:GLN:HE22 2.15 0.4311:K:764:HIS:CE1 11:K:767:LEU:HD13 2.53 0.4313:M:330:LEU:O 13:M:342:ASN:HB2 2.19 0.43
13:M:389:VAL:HG13 13:M:478:ALA:HA 1.99 0.435:E:123:THR:O 5:E:123:THR:HG22 2.18 0.435:E:196:ASN:O 5:E:231:THR:HG22 2.18 0.437:G:66:VAL:CG1 7:G:99:VAL:HG23 2.48 0.438:H:39:PHE:CD1 8:H:65:LYS:HD2 2.53 0.4311:K:430:THR:O 11:K:433:LEU:HG 2.19 0.4311:K:492:CYS:SG 11:K:500:LEU:HD13 2.59 0.434:D:170:THR:HG22 4:D:171:SER:N 2.34 0.438:H:36:ASP:HB2 8:H:39:PHE:CE2 2.54 0.434:D:111:HIS:O 4:D:114:THR:HG22 2.19 0.43
6:F:45:LEU:HD11 10:J:638:PHE:CD1 2.54 0.4313:M:129:VAL:O 13:M:129:VAL:HG23 2.19 0.432:B:93:ARG:HG2 2:B:93:ARG:O 2.18 0.433:C:103:GLN:OE1 4:D:92:LYS:HD2 2.19 0.43
13:M:1007:MET:HB3 13:M:1023:PHE:CE2 2.54 0.4315:O:43:A:OP2 15:O:43:A:C8 2.72 0.431:A:192:ILE:CD1 1:A:258:VAL:HG22 2.49 0.433:C:23:ARG:HB3 3:C:24:PRO:HD2 2.01 0.434:D:68:LYS:O 4:D:75:THR:HG21 2.19 0.43
9:I:155:VAL:HG23 9:I:163:GLN:NE2 2.33 0.4311:K:485:ASP:OD2 11:K:531:TYR:OH 2.35 0.4311:K:721:LEU:O 11:K:725:LEU:HD23 2.19 0.43
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Page 31 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
11:K:855:VAL:HG23 11:K:855:VAL:O 2.19 0.4313:M:403:ALA:O 13:M:407:THR:HG23 2.18 0.438:H:63:VAL:O 8:H:65:LYS:N 2.52 0.429:I:158:SER:OG 9:I:159:GLU:N 2.52 0.42
11:K:68:PRO:HG2 11:K:73:LEU:HD21 2.00 0.4213:M:191:ILE:HG22 13:M:192:LYS:N 2.33 0.4213:M:340:GLU:O 13:M:344:ASN:N 2.41 0.4213:M:910:SER:HA 13:M:913:VAL:HG22 2.01 0.4213:M:262:ARG:NH1 15:O:20:C:O2’ 2.52 0.421:A:86:ALA:HB3 1:A:90:PHE:CD2 2.55 0.422:B:231:VAL:O 2:B:235:VAL:HG23 2.19 0.42
3:C:163:VAL:HG13 3:C:163:VAL:O 2.19 0.4211:K:103:ALA:HB3 11:K:104:PRO:HD3 1.99 0.428:H:88:ILE:CD1 8:H:135:LEU:HG 2.50 0.4211:K:790:LEU:O 11:K:793:VAL:HG12 2.19 0.4213:M:455:HIS:NE2 13:M:464:LYS:HG3 2.34 0.421:A:61:CYS:SG 1:A:160:PHE:CE2 3.13 0.425:E:115:ASN:O 6:F:230:GLU:HG2 2.19 0.42
8:H:146:GLN:HB2 8:H:157:HIS:ND1 2.33 0.4211:K:201:LEU:O 11:K:202:THR:HG22 2.19 0.42
11:K:506:ILE:HG22 11:K:507:ALA:N 2.34 0.4213:M:157:VAL:HG22 13:M:158:LEU:N 2.33 0.4213:M:322:PRO:HB3 13:M:350:LEU:CD1 2.49 0.4213:M:599:PRO:O 13:M:603:GLU:N 2.44 0.421:A:23:ARG:NH2 1:A:213:GLU:OE1 2.52 0.421:A:76:LEU:HD12 1:A:116:ILE:CD1 2.49 0.427:G:249:ILE:HG23 7:G:268:ILE:HG23 2.00 0.427:G:86:LEU:HD12 7:G:101:TRP:O 2.20 0.428:H:247:GLN:HG3 8:H:281:VAL:HG21 2.02 0.424:D:80:LEU:HD23 4:D:81:ARG:N 2.34 0.427:G:163:ILE:CG2 7:G:164:TYR:N 2.83 0.4211:K:109:ILE:O 11:K:113:THR:HG23 2.20 0.42
2:B:184:LEU:HD12 2:B:200:MET:SD 2.60 0.424:D:194:MET:SD 4:D:195:SER:N 2.93 0.424:D:92:LYS:O 4:D:95:GLU:HG2 2.19 0.42
8:H:241:ILE:HG23 8:H:251:LEU:HD11 2.01 0.421:A:50:LEU:H 1:A:50:LEU:HD23 1.85 0.42
1:A:77:PHE:HE2 1:A:133:ARG:NH2 2.17 0.423:C:77:GLY:CA 3:C:132:VAL:HG22 2.49 0.42
4:D:181:LEU:HD23 4:D:197:THR:CB 2.49 0.425:E:112:ILE:O 5:E:112:ILE:HG22 2.20 0.42
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Page 32 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:35:ARG:NH1 6:F:198:ASP:O 2.46 0.427:G:147:GLU:HA 7:G:181:ILE:HD12 2.02 0.427:G:229:ILE:HG22 7:G:239:VAL:HG12 2.02 0.4213:M:279:TYR:CE2 13:M:281:PHE:CZ 3.07 0.4213:M:382:MET:HG2 13:M:411:PHE:CE1 2.54 0.4215:O:16:DT:H4’ 15:O:17:C:OP1 2.19 0.427:G:124:LYS:HA 7:G:129:PHE:HA 2.02 0.4211:K:194:CYS:O 11:K:198:VAL:HG12 2.19 0.42
11:K:529:THR:OG1 11:K:780:ARG:HG3 2.20 0.4211:K:719:LYS:O 11:K:720:SER:C 2.57 0.42
13:M:236:LEU:HD12 13:M:272:LEU:HB3 2.02 0.421:A:78:PHE:CE1 1:A:110:LEU:HD22 2.54 0.423:C:88:LEU:HB2 6:F:65:ALA:HB3 2.02 0.424:D:40:ARG:N 4:D:41:PRO:HD2 2.35 0.426:F:67:SER:HB2 6:F:145:GLU:HB2 2.02 0.427:G:249:ILE:CG2 7:G:272:LEU:HD21 2.50 0.429:I:63:LEU:HD13 9:I:95:LEU:HD13 2.02 0.4211:K:161:LYS:HA 11:K:166:ASP:OD1 2.20 0.421:A:24:LEU:HD13 7:G:248:LEU:HD22 2.01 0.413:C:190:ARG:N 3:C:190:ARG:HD2 2.34 0.414:D:36:ASN:ND2 4:D:143:ASP:OD2 2.53 0.415:E:33:ARG:NE 5:E:213:ASP:OD2 2.53 0.41
13:M:869:VAL:HG22 13:M:870:ILE:N 2.34 0.411:A:134:VAL:HG13 1:A:134:VAL:O 2.19 0.412:B:158:ALA:HB2 2:B:187:ALA:HB2 2.01 0.412:B:23:LYS:O 2:B:23:LYS:HG3 2.20 0.41
7:G:34:LEU:HD23 7:G:78:LEU:O 2.20 0.417:G:35:LEU:H 7:G:35:LEU:HD23 1.86 0.41
9:I:126:ASP:OD2 9:I:183:ARG:NH1 2.52 0.419:I:43:LYS:O 9:I:43:LYS:HG3 2.20 0.41
11:K:386:GLU:HG3 11:K:386:GLU:O 2.20 0.4111:K:571:GLU:OE1 11:K:571:GLU:N 2.53 0.4113:M:187:PHE:HD2 13:M:226:VAL:HG13 1.86 0.41
1:A:33:ARG:O 1:A:35:ILE:HG23 2.21 0.412:B:124:VAL:HG11 2:B:137:CYS:HB3 2.02 0.413:C:11:LEU:HD21 3:C:15:ARG:NH1 2.34 0.415:E:284:ARG:NH2 8:H:8:PRO:O 2.53 0.416:F:50:LYS:HE2 6:F:172:ALA:O 2.20 0.4111:K:763:HIS:HA 11:K:770:PRO:HA 2.01 0.4113:M:834:SER:O 13:M:838:GLU:OE1 2.39 0.41
6:F:211:LEU:HD23 6:F:212:THR:N 2.36 0.41Continued on next page...
Page 33 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Continued from previous page...
Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
6:F:215:LEU:HD21 6:F:248:CYS:CB 2.50 0.411:A:9:CYS:SG 7:G:197:GLY:O 2.79 0.41
11:K:495:LEU:HD23 11:K:496:GLU:N 2.35 0.411:A:75:ILE:CG2 1:A:76:LEU:N 2.83 0.411:A:281:LYS:HE3 4:D:51:ASP:OD1 2.21 0.416:F:126:LEU:HD23 6:F:162:LEU:HD23 2.02 0.413:C:143:ASP:OD1 6:F:46:LEU:HD22 2.20 0.419:I:130:ALA:HB1 9:I:145:THR:O 2.20 0.4111:K:285:ARG:O 11:K:285:ARG:HG3 2.20 0.4111:K:9:LYS:HD3 11:K:19:ILE:HD11 2.02 0.41
11:K:531:TYR:CE1 15:O:62:A:H2’ 2.56 0.411:A:24:LEU:HD22 1:A:24:LEU:N 2.35 0.413:C:28:GLU:HG3 3:C:28:GLU:O 2.20 0.415:E:23:ARG:NH2 5:E:218:GLU:OE1 2.52 0.416:F:138:ARG:HG3 6:F:175:GLU:OE1 2.21 0.417:G:229:ILE:CG2 7:G:239:VAL:HG12 2.50 0.415:E:35:VAL:CG1 8:H:5:MET:HG2 2.50 0.41
11:K:544:LEU:HD23 11:K:544:LEU:O 2.20 0.411:A:159:HIS:O 1:A:159:HIS:ND1 2.53 0.412:B:163:PHE:CZ 2:B:166:GLY:HA2 2.55 0.417:G:253:ILE:CG1 7:G:268:ILE:HG21 2.51 0.41
13:M:279:TYR:HE2 13:M:281:PHE:CZ 2.39 0.411:A:190:MET:O 1:A:190:MET:HG3 2.21 0.411:A:242:LEU:H 1:A:242:LEU:HD23 1.86 0.41
3:C:103:GLN:HB3 4:D:89:VAL:HG13 2.02 0.415:E:134:VAL:O 5:E:134:VAL:HG23 2.21 0.4111:K:64:HIS:NE2 11:K:197:TYR:CE1 2.89 0.4111:K:709:ARG:O 11:K:710:ASN:OD1 2.39 0.4111:K:774:HIS:C 11:K:784:ASP:OD1 2.59 0.4113:M:140:LEU:O 13:M:145:ARG:NH2 2.41 0.418:H:13:PRO:O 8:H:14:LEU:HB2 2.21 0.41
8:H:166:LEU:HD12 8:H:166:LEU:N 2.36 0.414:D:155:VAL:HG21 4:D:213:ALA:HB1 2.03 0.41
8:H:83:ILE:C 8:H:83:ILE:HD12 2.41 0.4111:K:36:CYS:HB2 11:K:159:HIS:NE2 2.36 0.41
11:K:509:VAL:HG12 11:K:513:ILE:HD12 2.03 0.4111:K:784:ASP:O 11:K:788:HIS:CD2 2.74 0.41
11:K:687:LEU:HD23 11:K:810:LEU:HD21 2.02 0.4111:K:850:ALA:HB1 11:K:862:VAL:HG22 2.01 0.4113:M:116:LEU:HD13 13:M:120:GLU:O 2.21 0.4113:M:512:ILE:HG22 13:M:551:LEU:HD11 2.03 0.41
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Page 34 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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Atom-1 Atom-2 Interatomicdistance (Å)
Clashoverlap (Å)
15:O:26:A:H2’ 15:O:27:C:O4’ 2.21 0.411:A:231:ILE:O 2:B:203:ARG:HA 2.20 0.41
8:H:119:GLU:OE1 8:H:121:ARG:NH1 2.54 0.418:H:63:VAL:O 8:H:64:ASN:C 2.59 0.419:I:16:ASN:OD1 9:I:32:TYR:CE1 2.74 0.4111:K:259:LEU:HA 11:K:283:LEU:HD11 2.03 0.4111:K:479:ASP:HB2 11:K:486:ILE:HD12 2.03 0.4111:K:564:TRP:HD1 11:K:575:THR:HG22 1.86 0.417:G:72:ARG:NH1 12:L:60:GLU:OE1 2.53 0.417:G:226:PRO:HB3 12:L:78:ARG:HG3 2.03 0.4113:M:873:LYS:HG2 13:M:893:PHE:CE2 2.56 0.4113:M:911:CYS:SG 13:M:967:MET:SD 3.19 0.411:A:161:ARG:HB3 1:A:182:PRO:HB2 2.03 0.402:B:24:ILE:HG22 2:B:42:GLN:HG3 2.02 0.402:B:45:THR:HG22 2:B:46:LYS:N 2.35 0.40
2:B:57:ILE:O 2:B:57:ILE:HD12 2.21 0.405:E:164:ARG:HG2 5:E:191:ARG:HD3 2.02 0.401:A:195:SER:OG 1:A:220:LEU:HD11 2.22 0.4011:K:750:GLN:HA 15:O:58:A:OP1 2.20 0.4011:K:911:ILE:HG23 11:K:923:ILE:HG23 2.03 0.4013:M:128:ARG:NH1 13:M:132:ALA:HB2 2.37 0.4013:M:185:VAL:HG23 13:M:248:TRP:HB2 2.04 0.401:A:200:GLN:HB2 1:A:203:THR:OG1 2.22 0.403:C:72:ASP:OD1 3:C:73:ALA:N 2.54 0.40
3:C:179:VAL:HG11 6:F:17:PRO:HB2 2.03 0.407:G:245:GLN:O 7:G:249:ILE:HG12 2.21 0.409:I:46:GLU:HG2 9:I:47:ASN:N 2.36 0.4011:K:64:HIS:ND1 11:K:64:HIS:O 2.53 0.407:G:88:HIS:CG 7:G:89:LYS:N 2.89 0.40
11:K:455:MET:HG3 11:K:455:MET:O 2.21 0.4011:K:688:LEU:CD2 11:K:771:ILE:HG23 2.51 0.4013:M:206:PHE:O 13:M:207:GLN:HB2 2.21 0.4013:M:866:SER:O 13:M:867:SER:HB3 2.22 0.40
13:M:969:VAL:HG13 13:M:982:ILE:HG23 2.04 0.401:A:34:ASN:OD1 1:A:34:ASN:O 2.39 0.404:D:69:GLU:HA 4:D:75:THR:HG21 2.04 0.409:I:13:ARG:HB3 9:I:34:PHE:CE1 2.56 0.40
11:K:360:LEU:HD13 11:K:385:ILE:HD11 2.03 0.4011:K:103:ALA:HB1 11:K:365:ILE:HD11 2.04 0.4011:K:372:LEU:HD21 11:K:382:ARG:HD3 2.04 0.40
There are no symmetry-related clashes.
Page 35 Full wwPDB EM Validation Report EMD-7808, 6D6Q
5.3 Torsion angles i○
5.3.1 Protein backbone i○
In the following table, the Percentiles column shows the percent Ramachandran outliers of thechain as a percentile score with respect to all PDB entries followed by that with respect to all EMentries.
The Analysed column shows the number of residues for which the backbone conformation wasanalysed, and the total number of residues.
Mol Chain Analysed Favoured Allowed Outliers Percentiles
1 A 285/473 (60%) 263 (92%) 22 (8%) 0 100 100
2 B 239/249 (96%) 215 (90%) 24 (10%) 0 100 100
3 C 263/278 (95%) 237 (90%) 26 (10%) 0 100 100
4 D 206/237 (87%) 197 (96%) 9 (4%) 0 100 100
5 E 284/293 (97%) 249 (88%) 35 (12%) 0 100 100
6 F 248/272 (91%) 230 (93%) 18 (7%) 0 100 100
7 G 233/277 (84%) 211 (91%) 22 (9%) 0 100 100
8 H 285/296 (96%) 240 (84%) 45 (16%) 0 100 100
9 I 181/197 (92%) 159 (88%) 22 (12%) 0 100 100
10 J 9/761 (1%) 5 (56%) 4 (44%) 0 100 100
11 K 839/960 (87%) 752 (90%) 87 (10%) 0 100 100
12 L 64/162 (40%) 54 (84%) 10 (16%) 0 100 100
13 M 703/1045 (67%) 647 (92%) 56 (8%) 0 100 100
All All 3839/5500 (70%) 3459 (90%) 380 (10%) 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
1 A 252/411 (61%) 251 (100%) 1 (0%) 91 97Continued on next page...
Page 36 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Continued from previous page...Mol Chain Analysed Rotameric Outliers Percentiles
2 B 184/189 (97%) 182 (99%) 2 (1%) 73 88
3 C 227/237 (96%) 225 (99%) 2 (1%) 78 91
4 D 172/195 (88%) 172 (100%) 0 100 100
5 E 249/254 (98%) 247 (99%) 2 (1%) 81 92
6 F 179/188 (95%) 177 (99%) 2 (1%) 73 88
7 G 196/223 (88%) 195 (100%) 1 (0%) 88 95
8 H 251/257 (98%) 247 (98%) 4 (2%) 62 83
9 I 159/172 (92%) 159 (100%) 0 100 100
10 J 10/672 (2%) 10 (100%) 0 100 100
11 K 758/854 (89%) 753 (99%) 5 (1%) 84 93
12 L 63/148 (43%) 63 (100%) 0 100 100
13 M 618/911 (68%) 616 (100%) 2 (0%) 92 98
All All 3318/4711 (70%) 3297 (99%) 21 (1%) 86 95
All (21) residues with a non-rotameric sidechain are listed below:
Mol Chain Res Type1 A 217 MET2 B 22 ARG2 B 58 ARG3 C 33 ARG3 C 94 ARG5 E 33 ARG5 E 162 ASN6 F 31 ARG6 F 35 ARG7 G 18 ARG8 H 17 ARG8 H 95 ARG8 H 121 ARG8 H 183 LYS11 K 144 ARG11 K 156 TYR11 K 284 ASN11 K 569 ASN11 K 689 ARG13 M 243 MET13 M 347 MET
Page 37 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (10)such sidechains are listed below:
Mol Chain Res Type5 E 44 ASN7 G 116 HIS9 I 16 ASN11 K 170 GLN11 K 266 HIS11 K 601 ASN11 K 821 HIS11 K 837 GLN13 M 291 GLN13 M 300 HIS
5.3.3 RNA i○
Mol Chain Analysed Backbone Outliers Pucker Outliers14 N 12/16 (75%) 0 015 O 33/62 (53%) 14 (42%) 2 (6%)All All 45/78 (57%) 14 (31%) 2 (4%)
All (14) RNA backbone outliers are listed below:
Mol Chain Res Type15 O 24 C15 O 26 A15 O 29 C15 O 42 C15 O 43 A15 O 44 C15 O 45 C15 O 50 C15 O 51 A15 O 52 C15 O 53 A15 O 54 C15 O 58 A15 O 62 A
All (2) RNA pucker outliers are listed below:
Page 38 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Mol Chain Res Type15 O 42 C15 O 53 A
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○
Of 3 ligands modelled in this entry, 2 are monoatomic - leaving 1 for Mogul analysis.
In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are defined in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from theexpected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).
Mol Type Chain Res Link Bond lengths Bond anglesCounts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 2
18 ANP M 2001 - 24,29,33 1.57 3 (12%) 25,45,52 1.16 2 (8%)
In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number defined in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.’-’ means no outliers of that kind were identified.
Mol Type Chain Res Link Chirals Torsions Rings18 ANP M 2001 - - 5/9/32/38 0/3/3/3
All (3) bond length outliers are listed below:
Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)18 M 2001 ANP PB-O1B 6.30 1.56 1.4618 M 2001 ANP PB-O2B -2.58 1.49 1.5618 M 2001 ANP PB-O3A -2.26 1.56 1.59
Page 39 Full wwPDB EM Validation Report EMD-7808, 6D6Q
All (2) bond angle outliers are listed below:
Mol Chain Res Type Atoms Z Observed(o) Ideal(o)18 M 2001 ANP PA-O3A-PB -4.29 118.94 132.5618 M 2001 ANP C5-C6-N6 2.35 123.92 120.35
There are no chirality outliers.
All (5) torsion outliers are listed below:
Mol Chain Res Type Atoms18 M 2001 ANP C5’-O5’-PA-O1A18 M 2001 ANP C5’-O5’-PA-O2A18 M 2001 ANP O4’-C4’-C5’-O5’18 M 2001 ANP C3’-C4’-C5’-O5’18 M 2001 ANP C5’-O5’-PA-O3A
There are no ring outliers.
1 monomer is involved in 2 short contacts:
Mol Chain Res Type Clashes Symm-Clashes18 M 2001 ANP 2 0
The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identified as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identified by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identified rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not find sufficientequivalents in the CSD to analyse the geometry.
Page 40 Full wwPDB EM Validation Report EMD-7808, 6D6Q
Ligand ANP M 2001
Bond lengths Bond angles
Torsions Rings
5.7 Other polymers i○
There are no such residues in this entry.
5.8 Polymer linkage issues i○
There are no chain breaks in this entry.
Page 41 Full wwPDB EM Validation Report EMD-7808, 6D6Q
6 Map visualisation i○
This section contains visualisations of the EMDB entry EMD-7808. 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: 192 Y Index: 192 Z Index: 192
Page 42 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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: 173 Y Index: 193 Z Index: 200
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 0.025.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.
Page 43 Full wwPDB EM Validation Report EMD-7808, 6D6Q
6.5 Mask visualisation i○
This section was not generated. No masks/segmentation were deposited.
Page 44 Full wwPDB EM Validation Report EMD-7808, 6D6Q
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.
Page 45 Full wwPDB EM Validation Report EMD-7808, 6D6Q
7.2 Volume estimate i○
The volume at the recommended contour level is 149 nm3; this corresponds to an approximatemass of 134 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 46 Full wwPDB EM Validation Report EMD-7808, 6D6Q
7.3 Rotationally averaged power spectrum i○
*Reported resolution corresponds to spatial frequency of 0.290 Å−1
Page 47 Full wwPDB EM Validation Report EMD-7808, 6D6Q
8 Fourier-Shell correlation i○
Fourier-Shell Correlation (FSC) is the most commonly used method to estimate the resolution ofsingle-particle and subtomogram-averaged maps. The shape of the curve depends on the imposedsymmetry, mask and whether or not the two 3D reconstructions used were processed from acommon reference. The reported resolution is shown as a black line. A curve is displayed for thehalf-bit criterion in addition to lines showing the 0.143 gold standard cut-off and 0.5 cut-off.
8.1 FSC i○
*Reported resolution corresponds to spatial frequency of 0.290 Å−1
Page 48 Full wwPDB EM Validation Report EMD-7808, 6D6Q
8.2 Resolution estimates i○
Resolution estimate (Å) Estimation criterion (FSC cut-off)0.143 0.5 Half-bit
Reported by author 3.45 - -Author-provided FSC curve 3.47 4.05 3.55
Calculated* - - -
*Resolution estimate based on FSC curve calculated by comparison of deposited half-maps.
Page 49 Full wwPDB EM Validation Report EMD-7808, 6D6Q
9 Map-model fit i○
This section contains information regarding the fit between EMDB map EMD-7808 and PDBmodel 6D6Q. Per-residue inclusion information can be found in section 3 on page 10.
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 0.025at 50% 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.
Page 50 Full wwPDB EM Validation Report EMD-7808, 6D6Q
9.2 Atom inclusion i○
At the recommended contour level, 70% of all backbone atoms, 60% of all non-hydrogen atoms,are inside the map.