Full wwPDB EM Validation Report...

Full wwPDB EM Validation Report i○

Dec 15, 2020 – 12:19 PM JST

PDB ID : 5Z10EMDB ID : EMD-6865

Title : Structure of the mechanosensitive Piezo1 channelAuthors : Zhao, Q.; Zhou, H.; Chi, S.; Wang, Y.; Wang, J.; Geng, J.; Wu, K.; Liu, W.;

Zhang, T.; Dong, M.-Q.; Wang, J.; Li, X.; Xiao, B.Deposited on : 2017-12-22

Resolution : 3.97 Å(reported)

This is a Full wwPDB EM Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected] user guide is available at

https://www.wwpdb.org/validation/2017/EMValidationReportHelpwith specific help available everywhere you see the i○ symbol.

The following versions of software and data (see references i○) were used in the production of this report:

EMDB validation analysis : 0.0.0.dev61MolProbity : 4.02b-467

Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)Ideal geometry (proteins) : Engh & Huber (2001)

Ideal geometry (DNA, RNA) : Parkinson et al. (1996)Validation Pipeline (wwPDB-VP) : 2.15.1

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

Full wwPDB EM Validation Report EMD-6865, 5Z10

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 3.97 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 3826

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


2 Entry composition i○

There is only 1 type of molecule in this entry. The entry contains 29142 atoms, of which 0 arehydrogens 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 Piezo-type mechanosensitive ion channel component 1.

Mol Chain Residues Atoms AltConf Trace

1 A 1304 Total C N O S9714 6308 1666 1701 39 0 0

1 B 1304 Total C N O S9714 6308 1666 1701 39 0 0

1 C 1304 Total C N O S9714 6308 1666 1701 39 0 0

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


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: Piezo-type mechanosensitive ion channel component 1

Chain A:

MET

GLU

PRO

HIS

VAL

LEU

GLY

ALA

GLY

LEU

TYR

TRP

LEU

LEU

LEU

PRO

CYS

THR

LEU

LEU

ALA

ALA

SER

LEU

LEU

ARG

PHE

ASN

ALA

LEU

SER

LEU

VAL

TYR

LEU

LEU

PHE

LEU

LEU

LEU

LEU

PRO

TRP

LEU

PRO

GLY

PRO

SER

ARG

HIS

SER

ILE

PRO

GLY

HIS

THR

GLY

ARG

LEU

LEU

ARG

ALA

LEU

LEU

CYS

LEU

SER

LEU

LEU

PHE

LEU

VAL

ALA

HIS

LEU

ALA

PHE

GLN

ILE

CYS

LEU

HIS

THR

VAL

PRO

HIS

LEU

ASP

GLN

PHE

LEU

GLY

GLN

ASN

GLY

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LEU

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VAL

LYS

VAL

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HIS

ILE

GLY

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ARG

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ASP

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ILE

PHE

ASN

THR

THR

ARG

LEU

VAL

ALA

PRO

ASP

LEU

GLY

VAL

LEU

LEU

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LEU

CYS

LEU

GLY

LEU

CYS

GLY

ARG

LEU

THR

ARG

LYS

ALA

GLY

GLN

SER

ARG

ARG

THR

GLN

GLU

LEU

GLN

ASP

ASP

ASP

ASP

ASP

ASP

ASP

ASP

ASP

ASP

GLU

ASP

ILE

ASP

ALA

ALA

PRO

ALA

VAL

GLY

LEU

LYS

GLY

ALA

PRO

ALA

LEU

ALA

THR

LYS

ARG

ARG

LEU

TRP

LEU

ALA

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ARG

PHE

ARG

VAL

THR

ALA

HIS

TRP

LEU

LEU

MET

THR

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GLY

ARG

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LEU

VAL

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VAL

LEU

LEU

ALA

LEU

ALA

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ALA

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PRO

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ALA

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TYR

LEU

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VAL

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CYS

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CYS

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PHE

PRO

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LEU

GLY

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CYS

VAL

MET

VAL

SER

CYS

PHE

GLY

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HIS

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CYS

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CYS

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ASP

MET

LEU

PRO

PRO

GLY

ASN

ILE

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ARG

LEU

PHE

GLY

LEU

LYS

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PHE

VAL

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LEU

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TYR

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LEU

VAL

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LYS

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GLY

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LEU

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LEU

LEU

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TYR

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LEU

LYS

LEU

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LYS

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CYS

PRO

SER

GLU

LEU

ARG

LYS

GLU

THR

PRO

ARG

GLU

ASP

GLU

GLU

HIS

GLU

LEU

GLU

LEU

ASP

HIS

LEU

GLU

PRO

GLU

PRO

GLN

ALA

ARG

ASP

ALA

THR

GLN

GLY

GLU

MET

PRO

MET

THR

THR

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ASP

LEU

ASP

ASN

CYS

THR

VAL

HIS

VAL

LEU

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GLN

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PRO

VAL

ARG

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VAL

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LEU

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LEU

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ASP

GLN

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VAL

CYS

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LEU

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MET

VAL

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MET

TYR

HIS

SER

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LEU

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VAL

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LEU

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ALA

CYS

LEU

ILE

TRP

THR

VAL

ARG

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ARG

HIS

GLN

LEU

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MET

LEU

CYS

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PRO

CYS

ILE

LEU

LEU

TYR

GLY

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LEU

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TYR

VAL

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ALA

MET

GLU

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PRO

GLU

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ASP

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VAL

LYS

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VAL

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LEU

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PHE

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ASP

GLU

GLN

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LEU

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LEU

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VAL

S684

F687

�S6

88S6

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A699

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Q703

Y706

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08

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G

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ARG

GLN

ASP

ALA

VAL

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GLU

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PRO

LEU

LEU

GLU

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GLU

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GLU

GLU

VAL

PHE

ARG

GLU

ASP

GLY

GLN

SER

MET

ASP

GLY

PRO

HIS

GLN

ALA

THR

GLN

VAL

PRO

GLU

GLY

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ALA

SER

LYS

TRP

GLY

LEU

VAL

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ASP

ARG

LEU

L784

A787

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L807

�

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


K823

�

P841

S853

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L866

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P874

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CYS

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THR

ASN

LEU

GLN

PRO

LEU

GLU

ILE

ASN

GLN

SER

LEU

LEU

TYR

ARG

GLY

PRO

VAL

ASP

PRO

ALA

N910

R942

�

Q950

�H9

51GL

NGL

NAL

APR

OLE

UPR

OAL

AGL

NAL

AVA

L

CYS

ALA

ASP

G965

T966

R967

D971

K988

R102

4R1

025

R102

6

L103

2

Y103

6

F103

9

G105

3ME

TPR

OPR

OAL

ALE

UCY

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EAS

PTY

RPR

OTR

PAR

GTR

PSE

RLY

SAL

AIL

EPR

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TAS

NSE

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STR

PLE

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S110

5

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UTR

PGL

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GME

TAL

AGL

YIL

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RAS

PHI

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134

I114

0P1

141

N114

2F1

143

I114

4H1

145

C114

6

L115

0

V115

5

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159

V116

8

V117

1

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177

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G118

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L119

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193

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Q120

0

K120

1

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6

D121

1C1

212

L121

3I1

214

S122

8LE

ULE

USE

RCY

SVA

LPH

EVA

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PVA

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LCY

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TME

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PAR

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PCY

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LGL

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278

G127

9I1

280

F128

9

L129

2Q1

293

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4R1

295

H130

4

D130

8

E133

8

Q134

4

R134

7

R135

3

S136

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L140

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H140

3

S140

9

E142

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UAL

ALE

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OAR

GPR

OAL

AAL

AGL

NSE

RAL

APH

EGL

NME

TAL

ATY

RGL

NAL

ATR

PVA

LTH

RAS

NAL

AGL

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RVA

LLE

UAR

GGL

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GAR

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UAR

GAL

AAR

GGL

NGL

UAR

GAL

AGL

UGL

NLE

UAL

ASE

RGL

YGL

YAS

PLE

UAS

NPR

OAS

P

VAL

GLU

PRO

VAL

ASP

VAL

PRO

GLU

ASP

GLU

MET

ALA

GLY

ARG

SER

HIS

MET

MET

GLN

ARG

VAL

LEU

SER

THR

MET

GLN

F150

4

D151

4

T151

7

K152

5

L154

0

L155

9TY

RVA

LGL

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ASE

R

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GLY

LEU

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GLU

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LEU

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ASP

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LEU

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THR

GLY

TYR

ASN

THR

ARG

SER

GLY

SER

GLU

GLU

ILE

VAL

THR

ASP

ALA

GLY

ASP

LEU

GLN

ALA

GLY

THR

SER

LEU

HIS

GLY

SER

GLN

GLU

LEU

LEU

ALA

ASN

ALA

ARG

THR

ARG

MET

ARG

THR

A164

5

D165

1

L165

4H1

655

I165

6

L165

9

A166

2

R167

1T1

672

S168

7

I169

5

P171

1

V171

4F1

715

L171

6

R172

4P1

725

S172

6K1

727

R172

8

F174

7GL

NPH

EGL

YPH

EPH

EPR

OTR

PAS

NSE

RTY

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LVA

LLE

UAR

GAR

GTY

RGL

UAS

NLY

SPR

OTY

RPH

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E

LEU

GLY

LEU

GLU

LYS

T177

9D1

780

S178

1Y1

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H179

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797

L180

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UTR

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PHI

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USE

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VAL

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ARG

ASP

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GLY

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ARG

SER

LYS

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VAL

ILE

GLN

ASP

PRO

PRO

GLU

ASP

LEU

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PRO

ARG

HIS

THR

ARG

HIS

ILE

SER

ILE

ARG

PHE

ARG

ARG

ARG

LYS

GLU

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PRO

GLY

PRO

LYS

GLY

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ALA

VAL

MET

GLU

THR

GLU

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LYS

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THR

GLU

ARG

LYS

ARG

PRO

ARG

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LYS

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ARG

GLU

ARG

MET

LYS

ALA

ALA

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ARG

ARG

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CYS

VAL

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LEU

ALA

GLN

SER

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TYR

Q195

6

D197

5

D198

4

D198

7

W199

6AL

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EGL

Y

LYS

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SER

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ASP

ASP

Q201

5

F202

0

M202

3

Q202

7

R203

5A2

036

L203

7Y2

038

L203

9

Q205

0V2

051

I205

7

L206

5P2

066

ALA

VAL

THR

GLU

ARG

MET

PHE

SER

GLN

N207

6

W208

2

K208

6C2

087

I208

8

S209

3

R210

4

N210

8F2

109

L211

0

N211

8L2

119

L213

1

R213

5

T214

6L2

147

S214

8L2

149

S215

0N2

151

I216

4

R216

9

K217

9

K218

3K2

184

V218

7

L220

8

V221

7�

V222

0N2

221

D222

5

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9L2

230

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237

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8F2

239

Q224

5P2

246

T225

2

A225

5

P226

5�

L226

8A2

269

T228

3A2

284

Q228

5


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6

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308

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D231

4�

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4R2

325

V233

3E2

334

E233

8

A234

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346

N234

7S2

348

R235

1R2

352

A235

5Q2

356

L235

7L2

358

E235

9

Q236

4S2

365

I236

8

F237

2

Y237

5I2

376

R237

7

N238

0

N238

5P2

386

V238

7K2

388

Q238

9L2

390

E239

4

D239

7Y2

398

L239

9G2

400

V240

1R2

402

I240

3

Q240

4L2

405

R240

6

Q240

9V2

410

GLY

THR

GLY

ALA

SER

GLY

GLU

GLN

ALA

G242

0

S242

4D2

425

F242

6L2

427

E242

8

V243

1

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4Q2

435

D243

6

A243

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I244

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L246

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G246

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8

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4

V251

3

E251

8L2

519

E252

0L2

521

E252

2E2

523

R253

4S2

535

T253

8

K254

1

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5R2

546

E254

7


Chain B:

MET

GLU

PRO

HIS

VAL

LEU

GLY

ALA

GLY

LEU

TYR

TRP

LEU

LEU

LEU

PRO

CYS

THR

LEU

LEU

ALA

ALA

SER

LEU

LEU

ARG

PHE

ASN

ALA

LEU

SER

LEU

VAL

TYR

LEU

LEU

PHE

LEU

LEU

LEU

LEU

PRO

TRP

LEU

PRO

GLY

PRO

SER

ARG

HIS

SER

ILE

PRO

GLY

HIS

THR

GLY

ARG

LEU

LEU

ARG

ALA

LEU

LEU

CYS

LEU

SER

LEU

LEU

PHE

LEU

VAL

ALA

HIS

LEU

ALA

PHE

GLN

ILE

CYS

LEU

HIS

THR

VAL

PRO

HIS

LEU

ASP

GLN

PHE

LEU

GLY

GLN

ASN

GLY

SER

LEU

TRP

VAL

LYS

VAL

SER

GLN

HIS

ILE

GLY

VAL

THR

ARG

LEU

ASP

LEU

LYS

ASP

ILE

PHE

ASN

THR

THR

ARG

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147

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0

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4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C3 DepositorNumber of particles used 238529 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) 50 DepositorMinimum defocus (nm) 3000 DepositorMaximum defocus (nm) Not providedMagnification 22500 DepositorImage detector GATAN K2 SUMMIT (4k x 4k) DepositorMaximum map value 0.300 DepositorMinimum map value -0.193 DepositorAverage map value 0.001 DepositorMap value standard deviation 0.006 DepositorRecommended contour level 0.027 DepositorMap size (Å) 369.6, 369.6, 369.6 wwPDBMap dimensions 280, 280, 280 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.32, 1.32, 1.32 Depositor

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


5 Model quality i○

5.1 Standard geometry i○

The Z score for a bond length (or angle) is the number of standard deviations the observed valueis removed from the expected value. A bond length (or angle) with |Z| > 5 is considered anoutlier worth inspection. RMSZ is the root-mean-square of all Z scores of the bond lengths (orangles).

Mol Chain Bond lengths Bond anglesRMSZ #|Z| >5 RMSZ #|Z| >51 A 0.36 0/9920 0.59 3/13499 (0.0%)1 B 0.36 0/9920 0.59 3/13499 (0.0%)1 C 0.36 0/9920 0.59 3/13499 (0.0%)All All 0.36 0/29760 0.59 9/40497 (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 outliers1 A 0 21 B 0 21 C 0 2All All 0 6

There are no bond length outliers.

All (9) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)1 A 1987 ASP CB-CG-OD1 7.41 124.97 118.301 C 1987 ASP CB-CG-OD1 7.38 124.94 118.301 B 1987 ASP CB-CG-OD1 7.37 124.94 118.301 A 2434 LEU CA-CB-CG 6.45 130.13 115.301 B 2434 LEU CA-CB-CG 6.45 130.13 115.301 C 2434 LEU CA-CB-CG 6.43 130.08 115.301 A 1801 LEU CA-CB-CG 5.80 128.65 115.301 B 1801 LEU CA-CB-CG 5.80 128.65 115.301 C 1801 LEU CA-CB-CG 5.80 128.63 115.30

There are no chirality outliers.

All (6) planarity outliers are listed below:

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


Mol Chain Res Type Group1 A 1724 ARG Peptide1 A 1975 ASP Peptide1 B 1724 ARG Peptide1 B 1975 ASP Peptide1 C 1724 ARG Peptide1 C 1975 ASP 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 9714 0 8963 124 01 B 9714 0 8963 124 01 C 9714 0 8963 127 0All All 29142 0 26889 357 0

The all-atom clashscore is defined as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 6.

All (357) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)Clash

overlap (Å)1:A:2406:ARG:O 1:A:2428:GLU:HA 1.74 0.881:B:2406:ARG:O 1:B:2428:GLU:HA 1.74 0.871:C:2406:ARG:O 1:C:2428:GLU:HA 1.74 0.86

1:A:2035:ARG:HH21 1:A:2039:LEU:HD11 1.52 0.741:B:2035:ARG:HH21 1:B:2039:LEU:HD11 1.52 0.731:C:2035:ARG:HH21 1:C:2039:LEU:HD11 1.52 0.721:A:1695:ILE:HG21 1:A:1714:VAL:HG21 1.75 0.681:B:1695:ILE:HG21 1:B:1714:VAL:HG21 1.75 0.671:C:1695:ILE:HG21 1:C:1714:VAL:HG21 1.75 0.671:C:1140:ILE:HA 1:C:1143:PHE:HB2 1.78 0.661:B:1140:ILE:HA 1:B:1143:PHE:HB2 1.78 0.651:C:2376:ILE:HA 1:C:2386:PRO:HA 1.80 0.641:A:2376:ILE:HA 1:A:2386:PRO:HA 1.80 0.641:A:1140:ILE:HA 1:A:1143:PHE:HB2 1.78 0.641:B:1338:GLU:O 1:B:2104:ARG:NH1 2.31 0.64

Continued on next page...

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


Continued from previous page...


overlap (Å)1:C:1338:GLU:O 1:C:2104:ARG:NH1 2.31 0.641:B:2376:ILE:HA 1:B:2386:PRO:HA 1.80 0.631:A:2376:ILE:HB 1:A:2448:ILE:HG22 1.81 0.631:A:1338:GLU:O 1:A:2104:ARG:NH1 2.31 0.63

1:C:2404:GLN:HB2 1:C:2431:VAL:HB 1.82 0.621:B:2376:ILE:HB 1:B:2448:ILE:HG22 1.80 0.621:B:2404:GLN:HB2 1:B:2431:VAL:HB 1.81 0.611:C:2376:ILE:HB 1:C:2448:ILE:HG22 1.80 0.611:C:1987:ASP:OD1 1:C:2082:TRP:NE1 2.33 0.611:A:2404:GLN:HB2 1:A:2431:VAL:HB 1.81 0.611:B:2380:ASN:ND2 1:B:2452:LYS:O 2.34 0.611:A:1987:ASP:OD1 1:A:2082:TRP:NE1 2.33 0.601:B:1987:ASP:OD1 1:B:2082:TRP:NE1 2.33 0.601:C:1984:ASP:OD1 1:C:2027:GLN:NE2 2.34 0.601:A:1984:ASP:OD1 1:A:2027:GLN:NE2 2.34 0.601:B:1984:ASP:OD1 1:B:2027:GLN:NE2 2.34 0.601:A:2380:ASN:ND2 1:A:2452:LYS:O 2.34 0.601:A:1155:VAL:HA 1:A:1158:PHE:HB2 1.84 0.591:C:2380:ASN:ND2 1:C:2452:LYS:O 2.34 0.591:A:2387:VAL:HG12 1:A:2389:GLN:H 1.68 0.591:C:2387:VAL:HG12 1:C:2389:GLN:H 1.67 0.591:B:1155:VAL:HA 1:B:1158:PHE:HB2 1.84 0.591:C:1155:VAL:HA 1:C:1158:PHE:HB2 1.84 0.59

1:B:1024:ARG:HH12 1:B:1294:ARG:HE 1.52 0.581:A:1146:CYS:HB2 1:A:1662:ALA:HB2 1.86 0.581:B:2387:VAL:HG12 1:B:2389:GLN:H 1.67 0.581:A:1024:ARG:HH12 1:A:1294:ARG:HE 1.52 0.581:B:2169:ARG:NH2 1:B:2497:LEU:O 2.35 0.581:C:1024:ARG:HH12 1:C:1294:ARG:HE 1.52 0.581:A:2169:ARG:NH2 1:A:2497:LEU:O 2.35 0.571:C:2169:ARG:NH2 1:C:2497:LEU:O 2.35 0.571:A:2108:ASN:OD1 1:A:2135:ARG:NH2 2.38 0.571:C:1146:CYS:HB2 1:C:1662:ALA:HB2 1.86 0.571:B:2108:ASN:OD1 1:B:2135:ARG:NH2 2.38 0.571:A:2375:TYR:HA 1:A:2447:VAL:O 2.05 0.561:B:1146:CYS:HB2 1:B:1662:ALA:HB2 1.86 0.561:C:2108:ASN:OD1 1:C:2135:ARG:NH2 2.38 0.561:A:1188:CYS:O 1:A:1192:LEU:HB2 2.06 0.56

1:A:1344:GLN:OE1 1:A:1347:ARG:NH1 2.39 0.561:A:1559:LEU:HA 1:A:1654:LEU:HD13 1.88 0.561:A:1687:SER:O 1:A:1796:HIS:ND1 2.38 0.56





overlap (Å)1:B:2347:ASN:OD1 1:B:2352:ARG:NH2 2.39 0.561:B:2535:SER:OG 1:B:2538:THR:OG1 2.23 0.561:C:2375:TYR:HA 1:C:2447:VAL:O 2.05 0.561:B:1559:LEU:HA 1:B:1654:LEU:HD13 1.88 0.561:B:1194:PHE:HB3 1:B:1198:LEU:HD23 1.88 0.561:C:2347:ASN:OD1 1:C:2352:ARG:NH2 2.39 0.551:B:2375:TYR:HA 1:B:2447:VAL:O 2.05 0.551:A:1194:PHE:HB3 1:A:1198:LEU:HD23 1.88 0.551:A:1711:PRO:HA 1:A:1714:VAL:HB 1.89 0.551:C:1194:PHE:HB3 1:C:1198:LEU:HD23 1.88 0.551:C:2245:GLN:HG2 1:C:2246:PRO:HD3 1.88 0.551:A:2245:GLN:HG2 1:A:2246:PRO:HD3 1.88 0.551:C:1188:CYS:O 1:C:1192:LEU:HB2 2.06 0.551:C:1201:LYS:O 1:C:1206:GLN:NE2 2.40 0.55

1:A:2347:ASN:OD1 1:A:2352:ARG:NH2 2.39 0.551:B:1188:CYS:O 1:B:1192:LEU:HB2 2.06 0.55

1:B:1344:GLN:OE1 1:B:1347:ARG:NH1 2.39 0.551:C:1344:GLN:OE1 1:C:1347:ARG:NH1 2.39 0.551:A:1201:LYS:O 1:A:1206:GLN:NE2 2.40 0.551:B:1711:PRO:HA 1:B:1714:VAL:HB 1.89 0.551:B:1201:LYS:O 1:B:1206:GLN:NE2 2.40 0.54

1:C:1711:PRO:HA 1:C:1714:VAL:HB 1.89 0.541:A:2377:ARG:HA 1:A:2449:PHE:HB2 1.90 0.541:B:2245:GLN:HG2 1:B:2246:PRO:HD3 1.88 0.541:C:2377:ARG:HA 1:C:2449:PHE:HB2 1.90 0.541:B:703:GLN:O 1:B:708:HIS:N 2.40 0.54

1:A:2535:SER:OG 1:A:2538:THR:OG1 2.23 0.541:A:703:GLN:O 1:A:708:HIS:N 2.40 0.54

1:C:1559:LEU:HA 1:C:1654:LEU:HD13 1.88 0.541:A:2283:THR:HG23 1:A:2447:VAL:HG22 1.90 0.54

1:C:1687:SER:O 1:C:1796:HIS:ND1 2.38 0.541:C:2148:SER:OG 1:C:2149:LEU:N 2.41 0.541:A:1168:VAL:HA 1:A:1171:VAL:HG12 1.90 0.541:A:2148:SER:OG 1:A:2149:LEU:N 2.41 0.541:C:703:GLN:O 1:C:708:HIS:N 2.40 0.53

1:B:2377:ARG:HA 1:B:2449:PHE:HB2 1.90 0.531:B:2365:SER:HB3 1:B:2402:ARG:HD3 1.90 0.531:C:1168:VAL:HA 1:C:1171:VAL:HG12 1.90 0.531:A:2496:GLU:O 1:B:2534:ARG:NH1 2.42 0.531:B:1687:SER:O 1:B:1796:HIS:ND1 2.38 0.531:B:2545:GLU:O 1:B:2546:ARG:NH2 2.42 0.53





overlap (Å)1:B:2496:GLU:O 1:C:2534:ARG:NH1 2.42 0.53

1:C:2365:SER:HB3 1:C:2402:ARG:HD3 1.90 0.531:B:1716:LEU:HD11 1:B:2051:VAL:HG12 1.91 0.531:A:2534:ARG:NH1 1:C:2496:GLU:O 2.41 0.521:B:2148:SER:OG 1:B:2149:LEU:N 2.41 0.521:A:2356:GLN:HG3 1:A:2364:GLN:HG2 1.92 0.521:A:2545:GLU:O 1:A:2546:ARG:NH2 2.42 0.52

1:B:2356:GLN:HG3 1:B:2364:GLN:HG2 1.92 0.521:B:2283:THR:HG23 1:B:2447:VAL:HG22 1.90 0.521:C:2252:THR:HG23 1:C:2255:ALA:H 1.75 0.521:A:2365:SER:HB3 1:A:2402:ARG:HD3 1.90 0.521:C:2283:THR:HG23 1:C:2447:VAL:HG22 1.90 0.521:A:1403:HIS:ND1 1:A:1403:HIS:O 2.43 0.521:B:1403:HIS:ND1 1:B:1403:HIS:O 2.43 0.52

1:B:2252:THR:HG23 1:B:2255:ALA:H 1.75 0.521:C:2535:SER:OG 1:C:2538:THR:OG1 2.23 0.521:B:1168:VAL:HA 1:B:1171:VAL:HG12 1.90 0.521:C:1403:HIS:O 1:C:1403:HIS:ND1 2.43 0.521:C:2545:GLU:O 1:C:2546:ARG:NH2 2.42 0.521:A:2110:LEU:O 1:A:2118:ASN:ND2 2.42 0.52

1:B:2409:GLN:NE2 1:B:2425:ASP:OD2 2.43 0.511:C:1716:LEU:HD11 1:C:2051:VAL:HG12 1.91 0.511:A:2409:GLN:NE2 1:A:2425:ASP:OD2 2.43 0.511:C:2356:GLN:HG3 1:C:2364:GLN:HG2 1.91 0.511:C:2409:GLN:NE2 1:C:2425:ASP:OD2 2.43 0.511:A:2252:THR:HG23 1:A:2255:ALA:H 1.75 0.511:B:2220:VAL:HA 1:B:2452:LYS:HG3 1.93 0.50

1:A:1716:LEU:HD11 1:A:2051:VAL:HG12 1.91 0.501:A:2519:LEU:HD13 1:C:2183:LYS:HD3 1.93 0.501:C:2220:VAL:HA 1:C:2452:LYS:HG3 1.93 0.50

1:C:2513:VAL:HG11 1:C:2521:LEU:HB3 1.94 0.501:A:2471:VAL:HA 1:A:2474:VAL:HG12 1.93 0.501:B:2183:LYS:HD3 1:C:2519:LEU:HD13 1.94 0.501:B:2368:ILE:HG13 1:B:2401:VAL:HB 1.94 0.501:B:988:LYS:HD3 1:B:1026:ARG:HH12 1.77 0.501:C:1196:THR:O 1:C:1200:GLN:NE2 2.45 0.501:C:2372:PHE:O 1:C:2399:LEU:N 2.45 0.501:C:2471:VAL:HA 1:C:2474:VAL:HG12 1.93 0.501:A:2231:LYS:HA 1:A:2237:PRO:HA 1.94 0.501:B:2345:ALA:HB3 1:B:2348:SER:HB3 1.94 0.491:A:988:LYS:HD3 1:A:1026:ARG:HH12 1.77 0.49





overlap (Å)1:B:2513:VAL:HG11 1:B:2521:LEU:HB3 1.94 0.491:A:1196:THR:O 1:A:1200:GLN:NE2 2.45 0.49

1:A:1159:ARG:NH2 1:A:1308:ASP:OD2 2.46 0.491:C:1159:ARG:NH2 1:C:1308:ASP:OD2 2.46 0.491:C:988:LYS:HD3 1:C:1026:ARG:HH12 1.77 0.491:A:2372:PHE:O 1:A:2399:LEU:N 2.45 0.49

1:A:2513:VAL:HG11 1:A:2521:LEU:HB3 1.94 0.491:A:2534:ARG:HH12 1:C:2498:PRO:HD3 1.78 0.491:B:1196:THR:O 1:B:1200:GLN:NE2 2.45 0.49

1:B:1159:ARG:NH2 1:B:1308:ASP:OD2 2.46 0.491:B:2110:LEU:O 1:B:2118:ASN:ND2 2.42 0.491:A:2220:VAL:HA 1:A:2452:LYS:HG3 1.93 0.49

1:B:2221:ASN:HD21 1:B:2325:ARG:HB2 1.78 0.491:C:2368:ILE:HG13 1:C:2401:VAL:HB 1.94 0.491:A:2368:ILE:HG13 1:A:2401:VAL:HB 1.94 0.491:A:2268:LEU:HB3 1:A:2389:GLN:HG3 1.95 0.491:B:2231:LYS:HA 1:B:2237:PRO:HA 1.94 0.481:B:2268:LEU:HB3 1:B:2389:GLN:HG3 1.95 0.481:A:2338:GLU:OE1 1:A:2385:ASN:ND2 2.46 0.481:B:2372:PHE:O 1:B:2399:LEU:N 2.45 0.481:B:2471:VAL:HA 1:B:2474:VAL:HG12 1.93 0.481:C:2345:ALA:HB3 1:C:2348:SER:HB3 1.94 0.481:C:2221:ASN:HD21 1:C:2325:ARG:HB2 1.78 0.481:A:2221:ASN:HD21 1:A:2325:ARG:HB2 1.78 0.481:C:2231:LYS:HA 1:C:2237:PRO:HA 1.94 0.481:A:1403:HIS:NE2 1:A:2146:THR:O 2.40 0.481:A:2345:ALA:HB3 1:A:2348:SER:HB3 1.94 0.481:B:2338:GLU:OE1 1:B:2385:ASN:ND2 2.46 0.481:A:2183:LYS:HD3 1:B:2519:LEU:HD13 1.94 0.481:B:2498:PRO:HD3 1:C:2534:ARG:HH12 1.78 0.481:A:2057:ILE:HG12 1:A:2086:LYS:HD2 1.96 0.471:B:2225:ASP:HB2 1:B:2324:GLN:O 2.14 0.471:C:1651:ASP:OD1 1:C:1651:ASP:N 2.47 0.471:C:2057:ILE:HG12 1:C:2086:LYS:HD2 1.96 0.471:B:2057:ILE:HG12 1:B:2086:LYS:HD2 1.96 0.471:C:2110:LEU:O 1:C:2118:ASN:ND2 2.42 0.47

1:C:2338:GLU:OE1 1:C:2385:ASN:ND2 2.46 0.471:A:2147:LEU:HD23 1:A:2151:ASN:HB3 1.97 0.471:C:2147:LEU:HD23 1:C:2151:ASN:HB3 1.97 0.471:A:1032:LEU:O 1:A:1036:TYR:N 2.48 0.47

1:A:1651:ASP:OD1 1:A:1651:ASP:N 2.47 0.47Continued on next page...




overlap (Å)1:B:2147:LEU:HD23 1:B:2151:ASN:HB3 1.97 0.471:A:2225:ASP:HB2 1:A:2324:GLN:O 2.14 0.471:A:1141:PRO:HD3 1:A:1304:HIS:CG 2.50 0.471:A:1514:ASP:HA 1:A:1517:THR:HG22 1.97 0.471:B:1141:PRO:HD3 1:B:1304:HIS:CG 2.50 0.471:B:2436:ASP:N 1:B:2436:ASP:OD1 2.48 0.471:B:1403:HIS:NE2 1:B:2146:THR:O 2.40 0.461:B:2213:ILE:O 1:B:2457:SER:OG 2.27 0.461:B:1032:LEU:O 1:B:1036:TYR:N 2.48 0.461:C:1403:HIS:NE2 1:C:2146:THR:O 2.40 0.461:C:2184:LYS:HB3 1:C:2187:VAL:HB 1.97 0.461:C:2268:LEU:HB3 1:C:2389:GLN:HG3 1.95 0.461:A:2436:ASP:N 1:A:2436:ASP:OD1 2.48 0.46

1:B:2324:GLN:HG3 1:B:2334:GLU:HG2 1.98 0.461:C:1141:PRO:HD3 1:C:1304:HIS:CG 2.50 0.461:A:2184:LYS:HB3 1:A:2187:VAL:HB 1.97 0.461:C:2225:ASP:HB2 1:C:2324:GLN:O 2.14 0.461:A:2269:ALA:HB1 1:A:2390:LEU:HD13 1.98 0.461:A:2498:PRO:HD3 1:B:2534:ARG:HH12 1.79 0.461:B:1144:ILE:HA 1:B:1155:VAL:HG11 1.98 0.461:B:2493:MET:HA 1:C:2534:ARG:HG3 1.97 0.461:A:2236:GLU:HB2 1:A:2296:ILE:HD13 1.98 0.461:B:2050:GLN:NE2 1:B:2093:SER:OG 2.47 0.461:C:1514:ASP:HA 1:C:1517:THR:HG22 1.97 0.461:B:2269:ALA:HB1 1:B:2390:LEU:HD13 1.98 0.461:A:2324:GLN:HG3 1:A:2334:GLU:HG2 1.98 0.461:A:2420:GLY:O 1:A:2424:SER:N 2.49 0.461:B:967:ARG:NH1 1:B:1116:THR:O 2.49 0.461:B:1514:ASP:HA 1:B:1517:THR:HG22 1.97 0.461:A:2493:MET:HA 1:B:2534:ARG:HG3 1.98 0.461:C:2269:ALA:HB1 1:C:2390:LEU:HD13 1.98 0.461:B:2236:GLU:HB2 1:B:2296:ILE:HD13 1.98 0.451:B:2420:GLY:O 1:B:2424:SER:N 2.49 0.451:C:2535:SER:HG 1:C:2538:THR:HG1 1.55 0.451:A:967:ARG:NH1 1:A:1116:THR:O 2.49 0.451:C:2420:GLY:O 1:C:2424:SER:N 2.49 0.451:C:1032:LEU:O 1:C:1036:TYR:N 2.47 0.451:C:967:ARG:NH1 1:C:1116:THR:O 2.49 0.451:B:1353:ARG:NE 1:B:2518:GLU:OE2 2.41 0.451:A:971:ASP:HA 1:A:1150:LEU:HD11 1.99 0.45

1:C:2221:ASN:OD1 1:C:2325:ARG:NE 2.43 0.45Continued on next page...




overlap (Å)1:C:2324:GLN:HG3 1:C:2334:GLU:HG2 1.98 0.451:A:1144:ILE:HA 1:A:1155:VAL:HG11 1.98 0.451:B:2184:LYS:HB3 1:B:2187:VAL:HB 1.97 0.451:C:2285:GLN:HB3 1:C:2443:LEU:HG 1.99 0.451:A:2534:ARG:HG3 1:C:2493:MET:HA 1.98 0.451:C:971:ASP:HA 1:C:1150:LEU:HD11 1.99 0.45

1:B:1780:ASP:OD1 1:B:1780:ASP:N 2.48 0.441:C:1727:LYS:HG3 1:C:1728:ARG:HG2 1.99 0.441:C:2309:TYR:OH 1:C:2359:GLU:OE2 2.35 0.441:C:2236:GLU:HB2 1:C:2296:ILE:HD13 1.98 0.441:B:1651:ASP:OD1 1:B:1651:ASP:N 2.47 0.441:C:1780:ASP:OD1 1:C:1780:ASP:N 2.48 0.441:C:2538:THR:HG22 1:C:2541:LYS:HE3 2.00 0.441:A:2406:ARG:HD3 1:A:2406:ARG:HA 1.83 0.441:B:1727:LYS:HG3 1:B:1728:ARG:HG2 1.99 0.441:C:2436:ASP:N 1:C:2436:ASP:OD1 2.48 0.441:A:1409:SER:O 1:A:1409:SER:OG 2.36 0.44

1:A:2285:GLN:HB3 1:A:2443:LEU:HG 1.99 0.441:B:2538:THR:HG22 1:B:2541:LYS:HE3 2.00 0.441:C:1144:ILE:HA 1:C:1155:VAL:HG11 1.98 0.441:C:1289:PHE:HD1 1:C:1292:LEU:HD12 1.83 0.441:A:2309:TYR:OH 1:A:2359:GLU:OE2 2.35 0.441:A:2397:ASP:N 1:A:2397:ASP:OD1 2.50 0.44

1:A:2538:THR:HG22 1:A:2541:LYS:HE3 2.00 0.441:C:2050:GLN:NE2 1:C:2093:SER:OG 2.47 0.441:B:593:MET:O 1:B:597:VAL:CB 2.66 0.441:A:1726:SER:OG 1:A:1728:ARG:N 2.52 0.431:B:2309:TYR:OH 1:B:2359:GLU:OE2 2.35 0.431:C:1726:SER:OG 1:C:1728:ARG:N 2.51 0.431:A:1289:PHE:HD1 1:A:1292:LEU:HD12 1.83 0.431:B:1671:ARG:HG2 1:B:1672:THR:HG23 2.00 0.431:A:1671:ARG:HG2 1:A:1672:THR:HG23 2.00 0.431:C:2388:LYS:HD2 1:C:2394:GLU:HG2 1.99 0.431:A:1211:ASP:HA 1:A:1214:ILE:HG12 2.00 0.431:B:1656:ILE:HB 1:B:1659:LEU:HD13 2.00 0.431:B:2285:GLN:HB3 1:B:2443:LEU:HG 1.99 0.431:C:2410:VAL:HG21 1:C:2427:LEU:HD12 2.01 0.431:C:2461:LEU:HD12 1:C:2463:GLY:H 1.83 0.431:A:2410:VAL:HG21 1:A:2427:LEU:HD12 2.01 0.431:A:593:MET:O 1:A:597:VAL:CB 2.66 0.431:B:1726:SER:OG 1:B:1728:ARG:N 2.52 0.43





overlap (Å)1:B:2388:LYS:HD2 1:B:2394:GLU:HG2 1.99 0.431:C:2037:LEU:HD13 1:C:2037:LEU:HA 1.83 0.431:C:841:PRO:HA 1:C:1105:SER:HB2 2.01 0.431:A:841:PRO:HA 1:A:1105:SER:HB2 2.01 0.43

1:B:2295:ARG:HG2 1:B:2295:ARG:H 1.65 0.431:C:1353:ARG:NE 1:C:2518:GLU:OE2 2.41 0.431:B:2397:ASP:OD1 1:B:2397:ASP:N 2.50 0.431:C:2397:ASP:N 1:C:2397:ASP:OD1 2.50 0.43

1:A:2208:LEU:HD23 1:A:2208:LEU:HA 1.82 0.431:A:2388:LYS:HD2 1:A:2394:GLU:HG2 2.00 0.431:B:971:ASP:HA 1:B:1150:LEU:HD11 1.99 0.431:B:1211:ASP:HA 1:B:1214:ILE:HG12 2.00 0.43

1:B:2461:LEU:HD12 1:B:2463:GLY:H 1.83 0.431:A:1727:LYS:HG3 1:A:1728:ARG:HG2 1.99 0.431:A:2229:THR:OG1 1:A:2239:PHE:O 2.32 0.431:B:2410:VAL:HG21 1:B:2427:LEU:HD12 2.01 0.431:A:2461:LEU:HD12 1:A:2463:GLY:H 1.83 0.421:C:593:MET:O 1:C:597:VAL:CB 2.66 0.421:B:2372:PHE:HZ 1:B:2446:MET:HB3 1.84 0.421:C:2491:SER:OG 1:C:2491:SER:O 2.34 0.42

1:C:2521:LEU:HD12 1:C:2521:LEU:HA 1.90 0.421:A:2131:LEU:HA 1:A:2131:LEU:HD12 1.83 0.421:A:2372:PHE:HZ 1:A:2446:MET:HB3 1.84 0.421:B:1402:ASP:OD1 1:B:1402:ASP:N 2.52 0.421:A:2307:GLU:O 1:A:2351:ARG:NH2 2.53 0.421:A:2427:LEU:HA 1:A:2427:LEU:HD23 1.87 0.42

1:A:2521:LEU:HD12 1:A:2521:LEU:HA 1.90 0.421:C:2372:PHE:HZ 1:C:2446:MET:HB3 1.84 0.421:A:1402:ASP:OD1 1:A:1402:ASP:N 2.52 0.421:A:2221:ASN:OD1 1:A:2325:ARG:NE 2.43 0.421:C:1211:ASP:HA 1:C:1214:ILE:HG12 2.00 0.421:C:1671:ARG:HG2 1:C:1672:THR:HG23 2.00 0.421:A:1401:LEU:HD12 1:C:2179:LYS:HE2 2.01 0.421:A:1656:ILE:HB 1:A:1659:LEU:HD13 2.00 0.421:B:1289:PHE:HD1 1:B:1292:LEU:HD12 1.83 0.421:B:1540:LEU:HD13 1:B:1559:LEU:HD13 2.02 0.421:B:2131:LEU:HA 1:B:2131:LEU:HD12 1.83 0.421:B:1727:LYS:H 1:B:1727:LYS:HG2 1.53 0.421:B:2307:GLU:O 1:B:2351:ARG:NH2 2.53 0.421:C:2065:LEU:HA 1:C:2065:LEU:HD12 1.92 0.421:C:2307:GLU:O 1:C:2351:ARG:NH2 2.52 0.42





overlap (Å)1:C:1656:ILE:HB 1:C:1659:LEU:HD13 2.00 0.421:A:1036:TYR:HA 1:A:1039:PHE:CE1 2.55 0.411:A:2308:LEU:HD22 1:A:2358:LEU:HD21 2.02 0.411:B:1541:LEU:O 1:B:1545:LEU:N 2.52 0.411:B:841:PRO:HA 1:B:1105:SER:HB2 2.01 0.41

1:A:2065:LEU:HD12 1:A:2065:LEU:HA 1.92 0.411:A:2088:ILE:H 1:A:2088:ILE:HG13 1.69 0.41

1:B:1036:TYR:HA 1:B:1039:PHE:CE1 2.55 0.411:B:2230:LEU:HB3 1:B:2239:PHE:HB3 2.03 0.411:C:2119:LEU:HD11 1:C:2164:ILE:HG23 2.03 0.41

1:B:2088:ILE:H 1:B:2088:ILE:HG13 1.69 0.411:B:703:GLN:O 1:B:707:PHE:N 2.53 0.411:C:1541:LEU:O 1:C:1545:LEU:N 2.52 0.411:C:703:GLN:O 1:C:707:PHE:N 2.53 0.41

1:A:1353:ARG:NE 1:A:2518:GLU:OE2 2.41 0.411:B:2491:SER:O 1:B:2491:SER:OG 2.34 0.41

1:A:2179:LYS:HE2 1:B:1401:LEU:HD12 2.01 0.411:C:1727:LYS:HG2 1:C:1727:LYS:H 1.53 0.411:A:2504:LEU:HD12 1:A:2504:LEU:HA 1.94 0.411:B:2179:LYS:HE2 1:C:1401:LEU:HD12 2.02 0.411:B:2378:ALA:HB3 1:B:2450:SER:HA 2.03 0.411:C:1540:LEU:HD13 1:C:1559:LEU:HD13 2.02 0.411:C:1551:VAL:HG22 1:C:1554:GLY:H 1.86 0.411:A:2037:LEU:HD13 1:A:2037:LEU:HA 1.83 0.411:B:2059:ILE:HD13 1:B:2059:ILE:HA 1.89 0.411:B:2352:ARG:HD3 1:B:2355:ALA:HB3 2.03 0.411:C:2308:LEU:HD22 1:C:2358:LEU:HD21 2.03 0.411:A:2020:PHE:HA 1:A:2023:MET:HE2 2.02 0.401:A:2119:LEU:HD11 1:A:2164:ILE:HG23 2.03 0.401:B:2119:LEU:HD11 1:B:2164:ILE:HG23 2.03 0.401:C:2208:LEU:HD23 1:C:2208:LEU:HA 1.82 0.401:C:2352:ARG:HD3 1:C:2355:ALA:HB3 2.03 0.401:C:2406:ARG:HD3 1:C:2406:ARG:HA 1.83 0.401:A:2352:ARG:HD3 1:A:2355:ALA:HB3 2.03 0.401:C:2504:LEU:HA 1:C:2504:LEU:HD12 1.94 0.40

1:A:1540:LEU:HD13 1:A:1559:LEU:HD13 2.02 0.401:B:2020:PHE:HA 1:B:2023:MET:HE2 2.02 0.401:B:2179:LYS:HD3 1:C:1401:LEU:HB2 2.04 0.401:A:1213:LEU:HA 1:A:1213:LEU:HD12 1.96 0.401:A:2230:LEU:HB3 1:A:2239:PHE:HB3 2.03 0.401:B:2289:SER:HA 1:B:2431:VAL:HG13 2.03 0.40





overlap (Å)1:C:1036:TYR:HA 1:C:1039:PHE:CE1 2.55 0.401:C:1402:ASP:N 1:C:1402:ASP:OD1 2.52 0.40

1:C:2230:LEU:HB3 1:C:2239:PHE:HB3 2.03 0.401:C:2361:ARG:HA 1:C:2362:PRO:HD3 1.99 0.401:A:1401:LEU:HB2 1:C:2179:LYS:HD3 2.04 0.401:A:1403:HIS:NE2 1:A:2523:GLU:OE2 2.55 0.401:A:1780:ASP:OD1 1:A:1780:ASP:N 2.48 0.401:A:2050:GLN:NE2 1:A:2093:SER:OG 2.47 0.401:B:1331:ILE:HD13 1:B:1331:ILE:HA 1.93 0.401:B:2321:TRP:HD1 1:B:2323:PHE:HE2 1.69 0.401:B:2308:LEU:HD22 1:B:2358:LEU:HD21 2.03 0.401:B:2477:VAL:HG13 1:C:2130:PHE:HZ 1.86 0.401:C:2059:ILE:HD13 1:C:2059:ILE:HA 1.89 0.401:C:2088:ILE:H 1:C:2088:ILE:HG13 1.68 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 1270/2547 (50%) 1168 (92%) 102 (8%) 0 100 100

1 B 1270/2547 (50%) 1168 (92%) 102 (8%) 0 100 100

1 C 1270/2547 (50%) 1168 (92%) 102 (8%) 0 100 100

All All 3810/7641 (50%) 3504 (92%) 306 (8%) 0 100 100

There are no Ramachandran outliers to report.

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


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 883/2246 (39%) 876 (99%) 7 (1%) 81 88

1 B 883/2246 (39%) 876 (99%) 7 (1%) 81 88

1 C 883/2246 (39%) 876 (99%) 7 (1%) 81 88

All All 2649/6738 (39%) 2628 (99%) 21 (1%) 82 88

All (21) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 1178 SER1 A 1280 ILE1 A 1295 ARG1 A 1525 LYS1 A 1797 ARG1 A 2333 VAL1 A 2441 CYS1 B 1178 SER1 B 1280 ILE1 B 1295 ARG1 B 1525 LYS1 B 1797 ARG1 B 2333 VAL1 B 2441 CYS1 C 1178 SER1 C 1280 ILE1 C 1295 ARG1 C 1525 LYS1 C 1797 ARG1 C 2333 VAL1 C 2441 CYS

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (34)such sidechains are listed below:

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


Mol Chain Res Type1 A 1200 GLN1 A 1315 GLN1 A 1510 GLN1 A 1668 GLN1 A 1669 GLN1 A 1686 HIS1 A 2018 GLN1 A 2058 HIS1 A 2380 ASN1 A 2409 GLN1 A 2442 ASN1 B 1200 GLN1 B 1315 GLN1 B 1510 GLN1 B 1668 GLN1 B 1669 GLN1 B 1686 HIS1 B 2018 GLN1 B 2058 HIS1 B 2380 ASN1 B 2409 GLN1 B 2442 ASN1 C 1200 GLN1 C 1315 GLN1 C 1510 GLN1 C 1668 GLN1 C 1669 GLN1 C 1686 HIS1 C 1789 GLN1 C 2018 GLN1 C 2058 HIS1 C 2380 ASN1 C 2409 GLN1 C 2442 ASN

5.3.3 RNA i○

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains i○

There are no non-standard protein/DNA/RNA residues in this entry.

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


5.5 Carbohydrates i○

There are no monosaccharides in this entry.

5.6 Ligand geometry i○

There are no ligands in this entry.

5.7 Other polymers i○

There are no such residues in this entry.

5.8 Polymer linkage issues i○

There are no chain breaks in this entry.

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


6 Map visualisation i○

This section contains visualisations of the EMDB entry EMD-6865. 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: 140 Y Index: 140 Z Index: 140

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


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: 142 Y Index: 143 Z Index: 178

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 0.027.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.

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


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


7.2 Volume estimate i○

The volume at the recommended contour level is 535 nm3; this corresponds to an approximatemass of 483 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 0.252 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 0.252 Å−1

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#fsc_validationhttps://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-bitReported by author 3.97 - -

Author-provided FSC curve 3.98 4.80 4.12Calculated* - - -

*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-6865 and PDBmodel 5Z10. Per-residue inclusion information can be found in section 3 on page 4.

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 0.027at 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_fithttps://www.wwpdb.org/validation/2017/EMValidationReportHelp#map_model_overlay


9.2 Atom inclusion i○

At the recommended contour level, 95% of all backbone atoms, 86% of all non-hydrogen atoms,are inside the map.

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

Overall quality at a glanceEntry compositionResidue-property plotsExperimental informationModel qualityStandard geometryToo-close contactsTorsion anglesProtein backboneProtein sidechainsRNA

Non-standard residues in protein, DNA, RNA chainsCarbohydratesLigand geometryOther polymersPolymer linkage issues

Map visualisationOrthogonal projectionsPrimary map

Central slicesPrimary map

Largest variance slicesPrimary map

Orthogonal surface viewsPrimary map

Mask visualisation

Map analysisMap-value distributionVolume estimateRotationally averaged power spectrum

Fourier-Shell correlationFSCResolution estimates

Map-model fitMap-model overlayAtom inclusion

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