Full wwPDB EM Map/Model Validation Report O i · 2020. 5. 31. · Full wwPDB EM Map/Model Validation Report O i May 24, 2020 11:03 pm BST PDB ID : 6D6Q EMDB ID : EMD-7808 Title :

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

https://www.wwpdb.org/validation/2017/EMValidationReportHelp



https://www.wwpdb.org/validation/2017/EMValidationReportHelp#references

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...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#overall_quality


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


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



2 B 241 Total C N O S1824 1126 345 344 9 0 0


https://www.wwpdb.org/validation/2017/EMValidationReportHelp#entry_composition


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



3 C 265 Total C N O S2020 1272 337 397 14 0 0


Chain Residue Modelled Actual Comment ReferenceC -1 ASP - expression tag UNP Q96B26C 0 PRO - expression tag UNP Q96B26



4 D 208 Total C N O S1566 979 278 297 12 0 0


Chain Residue Modelled Actual Comment ReferenceD -1 SER - expression tag UNP Q9NQT4D 0 LEU - expression tag UNP Q9NQT4



5 E 286 Total C N O S2194 1373 374 432 15 0 0


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.



6 F 252 Total C N O S1859 1154 353 345 7 0 0



7 G 237 Total C N O S1806 1136 329 329 12 0 0


Chain Residue Modelled Actual Comment ReferenceG -1 ASP - expression tag UNP Q9NQT5G 0 PRO - expression tag UNP Q9NQT5G 225 HIS TYR variant UNP Q9NQT5



8 H 289 Total C N O S2263 1424 405 419 15 0 0


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.


9 I 183 Total C N O S1407 884 247 266 10 0 0


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.



10 J 11 Total C N O86 56 14 16 0 0


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.


11 K 853 Total C N O S6856 4329 1233 1260 34 0 0


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.


12 L 68 Total C N O S573 371 95 101 6 0 0



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.


13 M 709 Total C N O S5648 3589 963 1052 44 0 0


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’).


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).


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).


17 K 1 Total Zn1 1 0


• Molecule 18 is PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (three-letter code: ANP) (formula: C10H17N6O12P3).


18 M 1 Total C N O P27 10 6 9 2 0


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:

MET

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Chain C:

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#residue_plots


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• Molecule 6: Exosome complex component MTR3

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• Molecule 9: Exosome complex component CSL4

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• Molecule 10: Exosome component 10

Chain J:

SER

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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

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ILE

ILE

ASP

THR

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GLU

LEU

ARG

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ASP

MET

TYR

ILE

LEU

ASN

GLU

SER

LEU

THR

ASP

PRO

ALA

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VAL

LYS

VAL

PHE

HIS

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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

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VAL

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LYS

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TYR

GLN

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ALA

ASP

TRP

ARG

ILE

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PRO

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GLU

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MET

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ASP

LYS

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MET

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PRO

VAL

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VAL

VAL

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ARG

ASP

LYS

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ALA

ARG

ARG

GLU

ASP

GLU

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TYR

GLY

TYR

VAL

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PRO

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VAL

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VAL

ARG

GLN

GLN

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MET

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VAL

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VAL

LYS

LYS

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GLY

PRO

LEU

PRO

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ALA

GLU

ARG

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VAL

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PRO

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ASP

CYS

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ALA

PRO

PRO

ASP

GLY

TYR

PRO

ILE

ILE

PRO

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LYS

LYS

ARG

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LYS

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• Molecule 11: Exosome complex exonuclease RRP44

Chain K:

GLY

SER

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E22

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D28

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LYS

LYS

LYS

LYS

MET

LYS

LEU

GLY

LYS

• Molecule 12: M-phase phosphoprotein 6

Chain L:

ASP

PRO

MET

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LYS

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LYS

LYS

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ASP

• Molecule 13: Exosome RNA helicase MTR4

Chain M:


SER

GLY

ASP

MET

ALA

ASP

ALA

PHE

GLY

ASP

GLU

LEU

PHE

SER

VAL

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GLU

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VAL

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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

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#experimental_info


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...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#model_quality

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#standard_geometry


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


https://www.wwpdb.org/validation/2017/EMValidationReportHelp#close_contacts


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 from previous page...


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...




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





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





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





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...




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





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





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





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





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





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





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...




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





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.


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...

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#torsion_angles

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_backbone

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#protein_sidechains


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


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:

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#rna


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

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#nonstandard_residues_and_ligands




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.


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.


https://www.wwpdb.org/validation/2017/EMValidationReportHelp#polymer_linkage


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

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_visualisation

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_projections

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#central_slices


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.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#largest_variance_slices

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#orthogonal_views


6.5 Mask visualisation i○

This section was not generated. No masks/segmentation were deposited.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#masks


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_analysis

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_value_distribution


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.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#volume_estimate


7.3 Rotationally averaged power spectrum i○

*Reported resolution corresponds to spatial frequency of 0.290 Å−1

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#raps


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

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validation

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validation


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.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#resolution_estimates


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.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_fit

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_overlay


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.

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#atom_inclusion_by_contour

Documents

Full wwPDB EM Map/Model Validation Report O i · 2020. 5. 31. · Full wwPDB EM Map/Model Validation Report O i May 24, 2020 11:03 pm BST PDB ID : 6D6Q EMDB ID : EMD-7808 Title :