Full wwPDB/EMDataBank EM Map/Model Validation...

Full wwPDB/EMDataBank EM Map/Model ValidationReport i○

Aug 28, 2019 – 09:44 AM EDT

PDB ID : 6PXVEMDB ID: : EMD-20522

Title : Cryo-EM structure of full-length insulin receptor bound to 4 insulin. 3D re-finement was focused on the extracellular region.

Authors : Uchikawa, E.; Choi, E.; Shang, G.J.; Yu, H.T.; Bai, X.C.Deposited on : 2019-07-27

Resolution : 3.20 Å(reported)

This is a Full wwPDB/EMDataBank EM Map/Model Validation Reportfor a publicly released PDB/EMDB 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.

MolProbity : 4.02b-467Percentile statistics : 20171227.v01 (using entries in the PDB archive December 27th 2017)

Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et. al. (1996)

Validation Pipeline (wwPDB-VP) : 2.4

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



Page 2 Full wwPDB/EMDataBank EM Map/Model Validation Report 6PXV

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 3.20 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 136327 1886Ramachandran outliers 132723 1663

Sidechain outliers 132532 1531

The table below summarises the geometric issues observed across the polymeric chains. The red,orange, yellow and green segments on the bar indicate the fraction of residues that contain outliersfor >=3, 2, 1 and 0 types of geometric quality criteria. A grey segment represents the fractionof residues that are not modelled. The numeric value for each fraction is indicated below thecorresponding segment, with a dot representing fractions <=5%

Mol Chain Length Quality of chain

1 A 1354

1 C 1354

2 D 74

2 E 74

2 F 74

2 G 74

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


2 Entry composition i○

There are 2 unique types of molecules in this entry. The entry contains 14774 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 Insulin receptor.

Mol Chain Residues Atoms AltConf Trace

1 A 823 Total C N O S6664 4231 1149 1236 48 0 0

1 C 823 Total C N O S6664 4231 1149 1236 48 0 0

There are 36 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 960 PHE TYR conflict UNP P06213A 962 THR SER conflict UNP P06213A 1120 ASN ASP conflict UNP P06213A 1333 ALA ARG conflict UNP P06213A 1334 ALA ILE conflict UNP P06213A 1335 ALA LEU conflict UNP P06213A 1337 ALA LEU conflict UNP P06213A 1344 LEU - expression tag UNP P06213A 1345 GLU - expression tag UNP P06213A 1346 SER - expression tag UNP P06213A 1347 SER - expression tag UNP P06213A 1348 GLY - expression tag UNP P06213A 1349 LEU - expression tag UNP P06213A 1350 GLU - expression tag UNP P06213A 1351 VAL - expression tag UNP P06213A 1352 LEU - expression tag UNP P06213A 1353 PHE - expression tag UNP P06213A 1354 GLN - expression tag UNP P06213C 960 PHE TYR conflict UNP P06213C 962 THR SER conflict UNP P06213C 1120 ASN ASP conflict UNP P06213C 1333 ALA ARG conflict UNP P06213C 1334 ALA ILE conflict UNP P06213C 1335 ALA LEU conflict UNP P06213C 1337 ALA LEU conflict UNP P06213C 1344 LEU - expression tag UNP P06213

Continued on next page...

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


Continued from previous page...Chain Residue Modelled Actual Comment Reference

C 1345 GLU - expression tag UNP P06213C 1346 SER - expression tag UNP P06213C 1347 SER - expression tag UNP P06213C 1348 GLY - expression tag UNP P06213C 1349 LEU - expression tag UNP P06213C 1350 GLU - expression tag UNP P06213C 1351 VAL - expression tag UNP P06213C 1352 LEU - expression tag UNP P06213C 1353 PHE - expression tag UNP P06213C 1354 GLN - expression tag UNP P06213

• Molecule 2 is a protein called Insulin.

Mol Chain Residues Atoms AltConf Trace

2 D 48 Total C N O S376 238 61 71 6 0 0

2 E 48 Total C N O S376 238 61 71 6 0 0

2 F 44 Total C N O S347 220 56 65 6 0 0

2 G 44 Total C N O S347 220 56 65 6 0 0


3 Residue-property plots i○

These plots are drawn for all protein, RNA and DNA chains in the entry. The first graphic fora chain summarises the proportions of the various outlier classes displayed in the second graphic.The second graphic shows the sequence view annotated by issues in geometry. Residues are color-coded according to the number of geometric quality criteria for which they contain at least oneoutlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretches of 2 or more consecutiveresidues without any outlier are shown as a green connector. Residues present in the sample, butnot in the model, are shown in grey.

• Molecule 1: Insulin receptor

Chain A:

H1 R14

N15

L20

L23

I29

L49

V99

H100

L101

K102

N111

R114

K121

L125

Y144

I145

V146

T162

ALA

LYS

GLY

LYS

THR

N168

I174

N175

R181

L213

T223

R236

Y245

Y246

H247

C253

R270

ARG

GLN

GLY

C274

K283

M294

I321

Q328

E329

L330

T334

R345

L350

L354

E355

I361

K369

R372

R383

Y401

T422

Q423

H429

L436

I439

H440

A458

Y477

I478

R479

T480

S481

F482

R488

R498

D499

F518

ASP

GLY

GLN

ASP

ALA

CYS

GLY

SER

ASN

S528

R539

P549

R554

P558

W559

T560

Q561

T578

Y579

Y587

T590

D591

A592

T593

N594

P595

S596

V597

P598

L599

V604

I612

L613

P618

S619

D620

P621

N622

I625

V630

R634

Q635

D638

S639

E640

L641

F642

E643

K649

G650

L651

K652

L653

P654

S655

R656

THR

TRP

SER

PRO

PRO

PHE

GLU

SER

GLU

ASP

SER

GLN

LYS

HIS

ASN

GLN

SER

GLU

TYR

GLU

ASP

SER

ALA

GLY

GLU

CYS

CYS

SER

CYS

PRO

LYS

THR

ASP

SER

Q691

E697

K703

E706

H710

V713

F714

R717

PRO

SER

ARG

LYS

ARG

ARG

SER

LEU

GLY

ASP

VAL

GLY

ASN

VAL

THR

VAL

ALA

VAL

PRO

THR

VAL

ALA

ALA

PHE

PRO

ASN

THR

SER

SER

THR

SER

VAL

PRO

THR

SER

PRO

E754

E755

H756

T777

G778

Y779

R780

I781

E782

L783

Q784

A785

T790

P791

E792

S796

V797

A798

R804

E808

A811

I822

V828

H829

L830

M831

W832

P835

K836

E837

P838

L841

I842

Y849

R850

R851

E856

L859

C860

V861

K864

H865

F866

C872

L877

S878

P879

Y882

S883

V884

R885

I886

R887

L891

S896

W897

P900

T901

Y902

F903

Y904

V905

Y908

L909

D910

VAL

PRO

SER

ASN

ILE

ALA

LYS

ILE

ILE

ILE

GLY

PRO

LEU

ILE

PHE

VAL

PHE

LEU

PHE

SER

VAL

VAL

ILE

GLY

SER

ILE

TYR

LEU

PHE

LEU

ARG

LYS

ARG

GLN

PRO

ASP

GLY

PRO

LEU

GLY

PRO

LEU

TYR

ALA

SER

SER

ASN

PRO

GLU

PHE

LEU

THR

ALA

SER

ASP

VAL

PHE

PRO

CYS

SER

VAL

TYR

VAL

PRO

ASP

GLU

TRP

GLU

VAL

SER

ARG

GLU

LYS

ILE

THR

LEU

LEU

ARG

GLU

LEU

GLY

GLN

GLY

SER

PHE

GLY

MET

VAL

TYR

GLU

GLY

ASN

ALA

ARG

ASP

ILE

ILE

LYS

GLY

GLU

ALA

GLU

THR

ARG

VAL

ALA

VAL

LYS

THR

VAL

ASN

GLU

SER

ALA

SER

LEU

ARG

GLU

ARG

ILE

GLU

PHE

LEU

ASN

GLU

ALA

SER

VAL

MET

LYS

GLY

PHE

THR

CYS

HIS

HIS

VAL

VAL

ARG

LEU

LEU

GLY

VAL

VAL

SER

LYS

GLY

GLN

PRO

THR

LEU

VAL

VAL

MET

GLU

LEU

MET

ALA

HIS

GLY

ASP

LEU

LYS

SER

TYR

LEU

ARG

SER

LEU

ARG

PRO

GLU

ALA

GLU

ASN

ASN

PRO

GLY

ARG

PRO

PRO

PRO

THR

LEU

GLN

GLU

MET

ILE

GLN

MET

ALA

ALA

GLU

ILE

ALA

ASP

GLY

MET

ALA

TYR

LEU

ASN

ALA

LYS

LYS

PHE

VAL

HIS

ARG

ASN

LEU

ALA

ALA

ARG

ASN

CYS

MET

VAL

ALA

HIS

ASP

PHE

THR

VAL

LYS

ILE

GLY

ASP

PHE

GLY

MET

THR

ARG

ASP

ILE

TYR

GLU

THR

ASP

TYR

TYR

ARG

LYS

GLY

GLY

LYS

GLY

LEU

LEU

PRO

VAL

ARG

TRP

MET

ALA

PRO

GLU

SER

LEU

LYS

ASP

GLY

VAL

PHE

THR

THR

SER

SER

ASP

MET

TRP

SER

PHE

GLY

VAL

VAL

LEU

TRP

GLU

ILE

THR

SER

LEU

ALA

GLU

GLN

PRO

TYR

GLN

GLY

LEU

SER

ASN

GLU

GLN

VAL

LEU

LYS

PHE

VAL

MET

ASP

GLY

GLY

TYR

LEU

ASP

GLN

PRO

ASP

ASN

CYS

PRO

GLU

ARG

VAL

THR

ASP

LEU

MET

ARG

MET

CYS

TRP

GLN

PHE

ASN

PRO

LYS

MET

ARG

PRO

THR

PHE

LEU

GLU

ILE

VAL

ASN

LEU

LEU

LYS

ASP

ASP

LEU

HIS

PRO

SER

PHE

PRO

GLU

VAL

SER

PHE

PHE

HIS

SER

GLU

GLU

ASN

LYS

ALA

PRO

GLU

SER

GLU

GLU

LEU

GLU

MET

GLU

PHE

GLU

ASP

MET

GLU

ASN

VAL

PRO

LEU

ASP

ARG

SER

SER

HIS

CYS

GLN

ARG

GLU

GLU

ALA

GLY

GLY

ARG

ASP

GLY

GLY

SER

SER

LEU

GLY

PHE

LYS

ARG

SER

TYR

GLU

GLU

HIS

ILE

PRO

TYR

THR

HIS

MET

ASN

GLY

GLY

LYS

LYS

ASN

GLY

ALA

ALA

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


ALA

THR

ALA

PRO

ARG

SER

ASN

PRO

SER

LEU

GLU

SER

SER

GLY

LEU

GLU

VAL

LEU

PHE

GLN

• Molecule 1: Insulin receptor

Chain C:

H1 R14

L20

L23

I29

L49

V99

H100

L101

K102

N111

R114

L125

Y144

I145

V146

L147

E154

T162

ALA

LYS

GLY

LYS

THR

N168

I174

N175

R181

L213

T223

R236

Y245

Y246

H247

C253

R270

ARG

GLN

GLY

C274

K283

M294

I321

Q328

E329

L330

T334

R345

L350

L354

E355

I361

K369

R383

Y401

T422

Q423

H429

L436

I439

H440

A458

Y477

I478

R479

T480

S481

F482

R488

R498

D499

N514

F518

ASP

GLY

GLN

ASP

ALA

CYS

GLY

SER

ASN

S528

R539

P549

R554

P558

W559

T560

Q561

T578

Y579

Y587

T590

D591

A592

T593

N594

P595

S596

V597

P598

L599

V604

I612

L613

P618

S619

D620

P621

N622

I625

V630

R634

Q635

D638

S639

E640

L641

F642

E643

K649

G650

L651

K652

L653

P654

S655

R656

THR

TRP

SER

PRO

PRO

PHE

GLU

SER

GLU

ASP

SER

GLN

LYS

HIS

ASN

GLN

SER

GLU

TYR

GLU

ASP

SER

ALA

GLY

GLU

CYS

CYS

SER

CYS

PRO

LYS

THR

ASP

SER

Q691

E697

K703

E706

H710

V713

F714

R717

PRO

SER

ARG

LYS

ARG

ARG

SER

LEU

GLY

ASP

VAL

GLY

ASN

VAL

THR

VAL

ALA

VAL

PRO

THR

VAL

ALA

ALA

PHE

PRO

ASN

THR

SER

SER

THR

SER

VAL

PRO

THR

SER

PRO

E754

E755

H756

T777

G778

Y779

R780

I781

E782

L783

Q784

A785

T790

P791

E792

S796

V797

A798

R804

E808

A811

I822

V828

H829

L830

M831

W832

P835

K836

E837

P838

L841

I842

Y849

R850

R851

E856

L859

C860

V861

K864

H865

F866

C872

L877

S878

P879

Y882

S883

V884

R885

I886

R887

L891

S896

W897

P900

T901

Y902

F903

Y904

V905

Y908

L909

D910

VAL

PRO

SER

ASN

ILE

ALA

LYS

ILE

ILE

ILE

GLY

PRO

LEU

ILE

PHE

VAL

PHE

LEU

PHE

SER

VAL

VAL

ILE

GLY

SER

ILE

TYR

LEU

PHE

LEU

ARG

LYS

ARG

GLN

PRO

ASP

GLY

PRO

LEU

GLY

PRO

LEU

TYR

ALA

SER

SER

ASN

PRO

GLU

PHE

LEU

THR

ALA

SER

ASP

VAL

PHE

PRO

CYS

SER

VAL

TYR

VAL

PRO

ASP

GLU

TRP

GLU

VAL

SER

ARG

GLU

LYS

ILE

THR

LEU

LEU

ARG

GLU

LEU

GLY

GLN

GLY

SER

PHE

GLY

MET

VAL

TYR

GLU

GLY

ASN

ALA

ARG

ASP

ILE

ILE

LYS

GLY

GLU

ALA

GLU

THR

ARG

VAL

ALA

VAL

LYS

THR

VAL

ASN

GLU

SER

ALA

SER

LEU

ARG

GLU

ARG

ILE

GLU

PHE

LEU

ASN

GLU

ALA

SER

VAL

MET

LYS

GLY

PHE

THR

CYS

HIS

HIS

VAL

VAL

ARG

LEU

LEU

GLY

VAL

VAL

SER

LYS

GLY

GLN

PRO

THR

LEU

VAL

VAL

MET

GLU

LEU

MET

ALA

HIS

GLY

ASP

LEU

LYS

SER

TYR

LEU

ARG

SER

LEU

ARG

PRO

GLU

ALA

GLU

ASN

ASN

PRO

GLY

ARG

PRO

PRO

PRO

THR

LEU

GLN

GLU

MET

ILE

GLN

MET

ALA

ALA

GLU

ILE

ALA

ASP

GLY

MET

ALA

TYR

LEU

ASN

ALA

LYS

LYS

PHE

VAL

HIS

ARG

ASN

LEU

ALA

ALA

ARG

ASN

CYS

MET

VAL

ALA

HIS

ASP

PHE

THR

VAL

LYS

ILE

GLY

ASP

PHE

GLY

MET

THR

ARG

ASP

ILE

TYR

GLU

THR

ASP

TYR

TYR

ARG

LYS

GLY

GLY

LYS

GLY

LEU

LEU

PRO

VAL

ARG

TRP

MET

ALA

PRO

GLU

SER

LEU

LYS

ASP

GLY

VAL

PHE

THR

THR

SER

SER

ASP

MET

TRP

SER

PHE

GLY

VAL

VAL

LEU

TRP

GLU

ILE

THR

SER

LEU

ALA

GLU

GLN

PRO

TYR

GLN

GLY

LEU

SER

ASN

GLU

GLN

VAL

LEU

LYS

PHE

VAL

MET

ASP

GLY

GLY

TYR

LEU

ASP

GLN

PRO

ASP

ASN

CYS

PRO

GLU

ARG

VAL

THR

ASP

LEU

MET

ARG

MET

CYS

TRP

GLN

PHE

ASN

PRO

LYS

MET

ARG

PRO

THR

PHE

LEU

GLU

ILE

VAL

ASN

LEU

LEU

LYS

ASP

ASP

LEU

HIS

PRO

SER

PHE

PRO

GLU

VAL

SER

PHE

PHE

HIS

SER

GLU

GLU

ASN

LYS

ALA

PRO

GLU

SER

GLU

GLU

LEU

GLU

MET

GLU

PHE

GLU

ASP

MET

GLU

ASN

VAL

PRO

LEU

ASP

ARG

SER

SER

HIS

CYS

GLN

ARG

GLU

GLU

ALA

GLY

GLY

ARG

ASP

GLY

GLY

SER

SER

LEU

GLY

PHE

LYS

ARG

SER

TYR

GLU

GLU

HIS

ILE

PRO

TYR

THR

HIS

MET

ASN

GLY

GLY

LYS

LYS

ASN

GLY

ALA

ALA

ALA

THR

ALA

PRO

ARG

SER

ASN

PRO

SER

LEU

GLU

SER

SER

GLY

LEU

GLU

VAL

LEU

PHE

GLN

• Molecule 2: Insulin

Chain D:


PHE

V2 C19

G20

E21

R22

G23

F24

F25

Y26

T27

P28

LYS

THR

ARG

ARG

GLU

ALA

GLU

ASP

LEU

GLN

GLY

SER

LEU

GLN

PRO

LEU

ALA

LEU

GLU

GLY

SER

LEU

GLN

LYS

ARG

G56

S67

Q70

N76


Chain E:

PHE

V2 C19

G20

E21

R22

Y26

T27

P28

LYS

THR

ARG

ARG

GLU

ALA

GLU

ASP

LEU

GLN

GLY

SER

LEU

GLN

PRO

LEU

ALA

LEU

GLU

GLY

SER

LEU

GLN

LYS

ARG

G56

S67

Q70

N76


Chain F:

PHE

VAL

ASN

Q4 C7 H10

L17

V18

C19

G20

E21

R22

G23

F24

F25

Y26

THR

PRO

LYS

THR

ARG

ARG

GLU

ALA

GLU

ASP

LEU

GLN

GLY

SER

LEU

GLN

PRO

LEU

ALA

LEU

GLU

GLY

SER

LEU

GLN

LYS

ARG

G56

S67

L68

Y69

Q70

N76


Chain G:

PHE

VAL

ASN

Q4 L17

V18

C19

G20

E21

R22

Y26

THR

PRO

LYS

THR

ARG

ARG

GLU

ALA

GLU

ASP

LEU

GLN

GLY

SER

LEU

GLN

PRO

LEU

ALA

LEU

GLU

GLY

SER

LEU

GLN

LYS

ARG

G56

S67

L68

Y69

Q70

N76


4 Experimental information i○

Property Value SourceReconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C2 DepositorNumber of particles used 235707 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) Not provided DepositorMaximum defocus (nm) Not provided DepositorMagnification Not provided DepositorImage detector GATAN K2 IS (4k x 4k) 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| >2 RMSZ #|Z| >2

1 A 0.46 0/6828 0.69 0/92581 C 0.46 0/6828 0.70 0/92582 D 0.35 0/383 0.51 0/5182 E 0.35 0/383 0.51 0/5182 F 0.37 0/353 0.54 0/4752 G 0.37 0/353 0.54 0/475All All 0.45 0/15128 0.68 0/20502

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 11 C 0 1All All 0 2

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

All (2) planarity outliers are listed below:

Mol Chain Res Type Group1 A 578 THR Peptide1 C 578 THR 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 hydrogen

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

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

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


atoms 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 6664 0 6478 108 01 C 6664 0 6478 114 02 D 376 0 346 5 02 E 376 0 346 4 02 F 347 0 317 8 02 G 347 0 317 9 0All All 14774 0 14282 232 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 8.

All (232) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

1:C:482:PHE:CZ 1:C:593:THR:HG21 1.45 1.501:A:482:PHE:CZ 1:A:593:THR:HG21 1.58 1.361:A:482:PHE:CE1 1:A:593:THR:HB 1.60 1.331:C:482:PHE:CZ 1:C:593:THR:CG2 2.13 1.301:C:482:PHE:CE1 1:C:593:THR:CG2 2.14 1.301:A:482:PHE:HE1 1:A:593:THR:CB 1.45 1.281:C:482:PHE:CE1 1:C:593:THR:HB 1.74 1.231:C:482:PHE:HE1 1:C:593:THR:CB 1.52 1.211:A:559:TRP:HB2 1:A:592:ALA:HB2 1.25 1.141:C:482:PHE:CE1 1:C:593:THR:CB 2.29 1.121:A:482:PHE:CZ 1:A:593:THR:CG2 2.34 1.101:C:559:TRP:HB2 1:C:592:ALA:HB2 1.17 1.101:A:482:PHE:CE1 1:A:593:THR:CB 2.26 1.091:A:482:PHE:CE1 1:A:593:THR:CG2 2.35 1.081:A:559:TRP:HB2 1:A:592:ALA:CB 1.88 1.031:A:482:PHE:HZ 1:A:593:THR:HG21 0.91 1.021:C:482:PHE:HE1 1:C:593:THR:HB 1.06 0.971:A:482:PHE:HE1 1:A:593:THR:HB 0.80 0.941:C:482:PHE:CE1 1:C:593:THR:HG22 2.02 0.931:A:559:TRP:CB 1:A:592:ALA:HB2 2.04 0.881:C:482:PHE:HZ 1:C:593:THR:CG2 1.66 0.861:A:790:THR:HB 1:A:791:PRO:HD3 1.57 0.861:C:790:THR:HB 1:C:791:PRO:HD3 1.57 0.851:C:482:PHE:HE1 1:C:593:THR:CG2 1.69 0.851:C:482:PHE:HZ 1:C:593:THR:HG21 0.88 0.81



Continued from previous page...


Clashoverlap (Å)

1:C:559:TRP:HB2 1:C:592:ALA:CB 2.07 0.781:A:755:GLU:HG2 1:A:756:HIS:N 1.99 0.761:A:755:GLU:HG2 1:A:756:HIS:H 1.51 0.751:C:755:GLU:HG2 1:C:756:HIS:N 1.99 0.751:C:350:LEU:O 1:C:354:LEU:HB2 1.88 0.741:A:350:LEU:O 1:A:354:LEU:HB2 1.88 0.72

1:C:755:GLU:HG2 1:C:756:HIS:H 1.51 0.721:C:599:LEU:HD11 1:C:619:SER:HB3 1.72 0.721:A:599:LEU:HD11 1:A:619:SER:HB3 1.72 0.721:A:885:ARG:HE 1:A:897:TRP:HB3 1.56 0.701:C:885:ARG:HE 1:C:897:TRP:HB3 1.56 0.691:A:590:THR:OG1 1:A:591:ASP:N 2.27 0.681:C:482:PHE:CZ 1:C:593:THR:HG22 2.14 0.671:C:590:THR:OG1 1:C:591:ASP:N 2.27 0.671:C:785:ALA:H 1:C:796:SER:HB3 1.60 0.66

1:A:651:LEU:HD23 1:A:651:LEU:H 1.62 0.641:A:785:ALA:H 1:A:796:SER:HB3 1.60 0.64

1:A:597:VAL:HG22 1:A:797:VAL:CG2 2.28 0.641:C:651:LEU:H 1:C:651:LEU:HD23 1.62 0.63

1:A:808:GLU:HB2 1:A:811:ALA:HB2 1.80 0.631:C:808:GLU:HB2 1:C:811:ALA:HB2 1.81 0.631:C:597:VAL:HG22 1:C:797:VAL:CG2 2.28 0.621:C:559:TRP:CB 1:C:592:ALA:HB2 2.10 0.621:C:879:PRO:HA 1:C:905:VAL:HG23 1.82 0.611:A:879:PRO:HA 1:A:905:VAL:HG23 1.82 0.61

1:C:223:THR:HG22 1:C:236:ARG:HG2 1.82 0.611:A:643:GLU:HA 1:A:864:LYS:HE3 1.82 0.60

1:A:223:THR:HG22 1:A:236:ARG:HG2 1.82 0.601:C:643:GLU:HA 1:C:864:LYS:HE3 1.82 0.601:C:593:THR:O 1:C:594:ASN:O 2.20 0.59

1:A:558:PRO:HB3 1:A:592:ALA:HA 1.84 0.591:C:422:THR:HG22 1:C:423:GLN:HG3 1.86 0.571:C:822:ILE:HG12 1:C:828:VAL:HG22 1.86 0.571:C:482:PHE:HA 1:C:591:ASP:OD1 2.05 0.571:A:634:ARG:HD2 1:A:777:THR:HG21 1.87 0.561:A:422:THR:HG22 1:A:423:GLN:HG3 1.86 0.561:A:593:THR:O 1:A:622:ASN:HB2 2.05 0.56

1:A:822:ILE:HG12 1:A:828:VAL:HG22 1.86 0.561:C:634:ARG:HD2 1:C:777:THR:HG21 1.87 0.561:C:885:ARG:NH1 1:C:900:PRO:HD3 2.21 0.561:A:604:VAL:HB 1:A:612:ILE:HG13 1.88 0.56





Clashoverlap (Å)

1:A:835:PRO:HD2 1:A:842:ILE:HD12 1.88 0.561:C:835:PRO:HD2 1:C:842:ILE:HD12 1.88 0.551:A:885:ARG:NH1 1:A:900:PRO:HD3 2.21 0.551:C:558:PRO:HB3 1:C:592:ALA:HA 1.88 0.551:C:499:ASP:OD1 1:C:703:LYS:NZ 2.37 0.551:C:604:VAL:HB 1:C:612:ILE:HG13 1.88 0.551:C:436:LEU:O 1:C:440:HIS:ND1 2.34 0.531:A:482:PHE:HA 1:A:591:ASP:OD1 2.08 0.531:A:593:THR:O 1:A:594:ASN:O 2.25 0.53

1:C:613:LEU:HD22 1:C:781:ILE:HG21 1.91 0.531:C:479:ARG:NH2 2:F:17:LEU:O 2.41 0.531:A:477:TYR:HB3 1:A:488:ARG:HB2 1.92 0.521:C:355:GLU:OE2 1:C:383:ARG:NH2 2.33 0.521:C:477:TYR:HB3 1:C:488:ARG:HB2 1.92 0.521:A:479:ARG:NH2 2:G:17:LEU:O 2.42 0.521:A:436:LEU:O 1:A:440:HIS:ND1 2.34 0.52

1:A:613:LEU:HD22 1:A:781:ILE:HG21 1.91 0.521:C:593:THR:O 1:C:622:ASN:HB2 2.10 0.522:F:67:SER:OG 2:F:70:GLN:NE2 2.43 0.52

1:A:654:PRO:HG2 1:A:656:ARG:HH21 1.73 0.521:A:499:ASP:OD1 1:A:703:LYS:NZ 2.36 0.521:C:654:PRO:HG2 1:C:656:ARG:HH21 1.73 0.521:A:355:GLU:OE2 1:A:383:ARG:NH2 2.33 0.512:D:67:SER:OG 2:D:70:GLN:NE2 2.43 0.512:G:67:SER:OG 2:G:70:GLN:NE2 2.43 0.511:A:482:PHE:CE1 1:A:593:THR:HG22 2.41 0.511:A:597:VAL:HG22 1:A:797:VAL:HG23 1.92 0.511:C:154:GLU:OE2 2:G:56:GLY:N 2.44 0.511:C:597:VAL:HG22 1:C:797:VAL:HG23 1.92 0.511:A:23:LEU:HD11 1:A:29:ILE:HD11 1.93 0.511:A:247:HIS:HB2 1:A:283:LYS:HG2 1.93 0.501:A:635:GLN:HE21 1:A:780:ARG:HB2 1.76 0.502:E:67:SER:OG 2:E:70:GLN:NE2 2.43 0.50

1:A:597:VAL:HG22 1:A:797:VAL:HG22 1.93 0.501:A:144:TYR:CE2 1:A:146:VAL:HG12 2.46 0.501:C:597:VAL:HG22 1:C:797:VAL:HG22 1.93 0.501:A:488:ARG:HE 2:G:68:LEU:HD21 1.77 0.501:A:630:VAL:HG22 1:A:783:LEU:HD13 1.94 0.501:C:482:PHE:CE1 1:C:593:THR:HG21 1.97 0.501:A:144:TYR:CE2 1:A:146:VAL:CG1 2.95 0.491:C:247:HIS:HB2 1:C:283:LYS:HG2 1.93 0.49





Clashoverlap (Å)

1:C:635:GLN:HE21 1:C:780:ARG:HB2 1.76 0.491:C:23:LEU:HD11 1:C:29:ILE:HD11 1.93 0.491:C:111:ASN:HD22 1:C:213:LEU:HD11 1.76 0.491:C:630:VAL:HG22 1:C:783:LEU:HD13 1.94 0.491:A:436:LEU:HD23 1:A:439:ILE:HD12 1.95 0.481:A:114:ARG:HH22 1:A:328:GLN:HE21 1.60 0.481:A:111:ASN:HD22 1:A:213:LEU:HD11 1.76 0.48

1:A:1:HIS:N 1:A:223:THR:O 2.37 0.481:A:877:LEU:N 1:A:877:LEU:HD12 2.29 0.48

1:C:114:ARG:HH22 1:C:328:GLN:HE21 1.60 0.481:A:481:SER:HB2 2:G:17:LEU:HD21 1.96 0.481:C:436:LEU:HD23 1:C:439:ILE:HD12 1.95 0.481:C:481:SER:HB2 2:F:17:LEU:HD21 1.96 0.481:A:593:THR:O 1:A:594:ASN:C 2.51 0.48

1:C:782:GLU:HG3 1:C:798:ALA:HB1 1.96 0.471:A:830:LEU:HB2 1:A:872:CYS:HB3 1.96 0.471:C:144:TYR:CE2 1:C:146:VAL:HG12 2.49 0.47

1:C:1:HIS:N 1:C:223:THR:O 2.37 0.472:E:67:SER:H 2:E:70:GLN:HE21 1.61 0.47

1:C:851:ARG:HB2 1:C:882:TYR:CE2 2.49 0.471:A:14:ARG:NH2 1:C:713:VAL:O 2.35 0.472:F:67:SER:H 2:F:70:GLN:HE21 1.61 0.47

1:A:559:TRP:HB2 1:A:592:ALA:HB3 1.88 0.471:A:481:SER:O 1:A:591:ASP:OD1 2.33 0.47

1:A:782:GLU:HG3 1:A:798:ALA:HB1 1.97 0.471:A:851:ARG:HB2 1:A:882:TYR:CE2 2.49 0.471:A:345:ARG:NH1 1:C:697:GLU:OE1 2.46 0.471:C:877:LEU:HD12 1:C:877:LEU:N 2.29 0.47

2:G:67:SER:H 2:G:70:GLN:HE21 1.61 0.472:D:67:SER:H 2:D:70:GLN:HE21 1.61 0.47

1:C:859:LEU:HD23 1:C:872:CYS:SG 2.55 0.472:E:19:CYS:SG 2:E:22:ARG:NH2 2.88 0.462:G:19:CYS:SG 2:G:22:ARG:NH2 2.88 0.461:A:706:GLU:O 1:A:710:HIS:ND1 2.45 0.462:D:19:CYS:SG 2:D:22:ARG:NH2 2.88 0.46

1:C:830:LEU:HB2 1:C:872:CYS:HB3 1.96 0.462:F:19:CYS:SG 2:F:22:ARG:NH2 2.88 0.461:C:334:THR:HA 1:C:361:ILE:HA 1.97 0.461:A:621:PRO:HB3 1:A:625:ILE:HD11 1.98 0.461:C:144:TYR:CE2 1:C:146:VAL:CG1 2.98 0.461:A:697:GLU:OE1 1:C:345:ARG:NH1 2.46 0.46





Clashoverlap (Å)

1:A:477:TYR:OH 2:G:21:GLU:OE2 2.34 0.461:C:481:SER:O 1:C:591:ASP:OD1 2.34 0.461:C:593:THR:O 1:C:594:ASN:C 2.54 0.46

1:C:885:ARG:HH12 1:C:900:PRO:HD3 1.81 0.461:C:498:ARG:NH1 1:C:706:GLU:OE1 2.48 0.451:A:334:THR:HA 1:A:361:ILE:HA 1.97 0.451:A:859:LEU:HD23 1:A:872:CYS:SG 2.55 0.451:C:706:GLU:O 1:C:710:HIS:ND1 2.45 0.452:F:24:PHE:CD2 2:F:26:TYR:HB2 2.51 0.452:G:26:TYR:CD1 2:G:26:TYR:C 2.90 0.45

1:A:885:ARG:HH12 1:A:900:PRO:HD3 1.81 0.451:C:621:PRO:HB3 1:C:625:ILE:HD11 1.98 0.451:C:828:VAL:HG21 1:C:903:PHE:CE1 2.51 0.451:A:713:VAL:O 1:C:14:ARG:NH2 2.35 0.45

1:A:861:VAL:HG12 1:A:866:PHE:HB2 1.99 0.451:A:828:VAL:HG21 1:A:903:PHE:CE1 2.52 0.441:C:369:LYS:HG3 1:C:401:TYR:HB3 1.99 0.441:A:498:ARG:NH1 1:A:706:GLU:OE1 2.48 0.441:A:369:LYS:HG3 1:A:401:TYR:HB3 1.99 0.441:C:832:TRP:HH2 1:C:872:CYS:HB2 1.82 0.441:A:832:TRP:HH2 1:A:872:CYS:HB2 1.82 0.441:A:849:TYR:HA 1:A:883:SER:O 2.17 0.441:C:755:GLU:CG 1:C:756:HIS:H 2.27 0.441:A:640:GLU:CD 1:A:640:GLU:H 2.21 0.441:A:641:LEU:HB3 1:A:841:LEU:HD21 1.99 0.44

2:F:7:CYS:O 2:F:10:HIS:HB2 2.18 0.441:C:641:LEU:HB3 1:C:841:LEU:HD21 1.99 0.441:C:850:ARG:NH2 1:C:856:GLU:HB2 2.33 0.431:C:849:TYR:HA 1:C:883:SER:O 2.17 0.431:C:861:VAL:HG12 1:C:866:PHE:HB2 1.99 0.431:C:102:LYS:HA 1:C:125:LEU:HA 2.00 0.431:A:651:LEU:CD2 1:A:651:LEU:H 2.30 0.431:A:710:HIS:HD2 1:A:714:PHE:HE2 1.66 0.431:A:144:TYR:HE2 1:A:146:VAL:HG12 1.83 0.431:C:429:HIS:CE1 1:C:458:ALA:HB2 2.54 0.431:A:832:TRP:CH2 1:A:872:CYS:HB2 2.54 0.431:A:850:ARG:NH2 1:A:856:GLU:HB2 2.33 0.431:C:640:GLU:H 1:C:640:GLU:CD 2.21 0.43

1:A:596:SER:HB3 1:A:618:PRO:HB2 2.01 0.431:C:778:GLY:HA2 1:C:804:ARG:HA 2.01 0.431:C:832:TRP:CH2 1:C:872:CYS:HB2 2.54 0.43





Clashoverlap (Å)

1:A:174:ILE:HB 1:A:181:ARG:HH22 1.84 0.431:C:596:SER:HB3 1:C:618:PRO:HB2 2.01 0.421:C:710:HIS:HD2 1:C:714:PHE:HE2 1.66 0.421:C:790:THR:HB 1:C:791:PRO:CD 2.40 0.421:A:654:PRO:HB2 1:A:656:ARG:HE 1.84 0.421:C:593:THR:O 1:C:622:ASN:CB 2.67 0.421:A:429:HIS:CE1 1:A:458:ALA:HB2 2.54 0.421:C:14:ARG:CZ 2:E:26:TYR:HB2 2.49 0.42

1:A:245:TYR:HB3 1:A:253:CYS:HB3 2.01 0.421:C:653:LEU:HD21 1:C:891:LEU:HD23 2.01 0.421:A:102:LYS:HA 1:A:125:LEU:HA 2.01 0.421:C:654:PRO:HB2 1:C:656:ARG:HE 1.84 0.421:A:561:GLN:HE21 1:A:587:TYR:HB3 1.85 0.421:A:778:GLY:HA2 1:A:804:ARG:HA 2.01 0.421:C:321:ILE:HD11 1:C:330:LEU:HD12 2.01 0.421:A:593:THR:O 1:A:622:ASN:CB 2.67 0.41

1:A:653:LEU:HD21 1:A:891:LEU:HD23 2.01 0.411:C:147:LEU:HD23 1:C:147:LEU:HA 1.93 0.411:C:558:PRO:CB 1:C:592:ALA:HA 2.50 0.411:C:514:ASN:OD1 1:C:514:ASN:N 2.51 0.411:C:174:ILE:HB 1:C:181:ARG:HH22 1.84 0.41

1:C:245:TYR:HB3 1:C:253:CYS:HB3 2.01 0.411:C:488:ARG:HE 2:F:68:LEU:HD21 1.84 0.411:A:15:ASN:HD21 2:D:24:PHE:H 1.68 0.411:C:887:ARG:HB2 1:C:897:TRP:CD2 2.56 0.411:A:321:ILE:HD11 1:A:330:LEU:HD12 2.01 0.411:C:561:GLN:HE21 1:C:587:TYR:HB3 1.85 0.411:C:598:PRO:HG2 1:C:783:LEU:HG 2.03 0.411:A:14:ARG:CZ 2:D:26:TYR:HB2 2.51 0.411:A:121:LYS:NZ 1:C:706:GLU:OE2 2.44 0.411:A:885:ARG:HE 1:A:897:TRP:CB 2.29 0.411:A:887:ARG:HB2 1:A:897:TRP:CD2 2.56 0.411:C:350:LEU:O 1:C:354:LEU:CB 2.65 0.41

1:A:345:ARG:HH21 1:A:372:ARG:HD2 1.86 0.411:C:99:VAL:HG12 1:C:100:HIS:CD2 2.56 0.411:C:597:VAL:HA 1:C:796:SER:HG 1.86 0.411:A:882:TYR:O 1:A:902:TYR:HA 2.21 0.40

1:A:20:LEU:HD23 1:A:49:LEU:HD21 2.03 0.401:C:755:GLU:CG 1:C:756:HIS:N 2.77 0.401:A:99:VAL:HG12 1:A:100:HIS:CD2 2.56 0.401:C:882:TYR:O 1:C:902:TYR:HA 2.21 0.40





Clashoverlap (Å)

1:A:144:TYR:HE2 1:A:146:VAL:CG1 2.33 0.401:C:20:LEU:HD23 1:C:49:LEU:HD21 2.03 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 811/1354 (60%) 719 (89%) 80 (10%) 12 (2%) 11 49

1 C 811/1354 (60%) 719 (89%) 79 (10%) 13 (2%) 11 47

2 D 44/74 (60%) 41 (93%) 2 (4%) 1 (2%) 7 38

2 E 44/74 (60%) 41 (93%) 2 (4%) 1 (2%) 7 38

2 F 40/74 (54%) 37 (92%) 2 (5%) 1 (2%) 6 36

2 G 40/74 (54%) 37 (92%) 2 (5%) 1 (2%) 6 36

All All 1790/3004 (60%) 1594 (89%) 167 (9%) 29 (2%) 15 47

All (29) Ramachandran outliers are listed below:

Mol Chain Res Type1 A 649 LYS1 A 790 THR1 A 896 SER1 C 649 LYS1 C 790 THR1 C 896 SER1 A 579 TYR1 A 638 ASP1 C 579 TYR1 C 594 ASN


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

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


Continued from previous page...Mol Chain Res Type1 C 638 ASP1 A 650 GLY1 C 650 GLY1 A 594 ASN1 A 792 GLU1 C 792 GLU1 A 836 LYS1 A 908 TYR1 C 590 THR1 C 836 LYS1 C 908 TYR1 A 838 PRO1 C 838 PRO1 A 549 PRO2 D 20 GLY2 E 20 GLY2 F 20 GLY2 G 20 GLY1 C 549 PRO

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 751/1209 (62%) 744 (99%) 7 (1%) 81 93

1 C 751/1209 (62%) 744 (99%) 7 (1%) 81 93

2 D 43/65 (66%) 43 (100%) 0 100 100

2 E 43/65 (66%) 43 (100%) 0 100 100

2 F 39/65 (60%) 39 (100%) 0 100 100

2 G 39/65 (60%) 39 (100%) 0 100 100

All All 1666/2678 (62%) 1652 (99%) 14 (1%) 84 94

All (14) residues with a non-rotameric sidechain are listed below:

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


Mol Chain Res Type1 A 175 ASN1 A 270 ARG1 A 294 MET1 A 539 ARG1 A 554 ARG1 A 638 ASP1 A 651 LEU1 C 175 ASN1 C 270 ARG1 C 294 MET1 C 539 ARG1 C 554 ARG1 C 638 ASP1 C 651 LEU

Some sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (27) suchsidechains are listed below:

Mol Chain Res Type1 A 15 ASN1 A 32 HIS1 A 34 GLN1 A 100 HIS1 A 175 ASN1 A 209 HIS1 A 546 GLN1 A 561 GLN1 A 610 GLN1 A 635 GLN1 C 15 ASN1 C 32 HIS1 C 34 GLN1 C 100 HIS1 C 175 ASN1 C 209 HIS1 C 546 GLN1 C 561 GLN1 C 610 GLN1 C 635 GLN2 D 3 ASN2 D 70 GLN2 E 3 ASN2 E 10 HIS2 E 70 GLN



Continued from previous page...Mol Chain Res Type2 F 70 GLN2 G 70 GLN

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.

5.5 Carbohydrates i○

There are no carbohydrates 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#rna

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




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

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