full wwpdb em map/model validation report o i · 2020. 8. 30. · page 4 ullf wwpdb em map/model...

Full wwPDB EM Validation Report i○

Dec 16, 2020 – 09:37 AM JST

PDB ID : 6KIWEMDB ID : EMD-0693

Title : Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom)Authors : Huang, J.; Xue, H.; Yao, T.

Deposited on : 2019-07-20Resolution : 4.00 Å(reported)

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

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

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

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

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

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

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

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-0693, 6KIW

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 4.00 Å.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

Metric Whole archive(#Entries)EM structures(#Entries)

Clashscore 158937 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


Continued from previous page...Mol Chain Length Quality of chain

5 I 144

6 J 145

7 K 205

8 N 538

9 O 76

10 R 334

11 T 534


2 Entry composition i○

There are 12 unique types of molecules in this entry. The entry contains 20225 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 Histone H3.

Mol Chain Residues Atoms AltConf Trace

1 A 97 Total C N O S802 506 155 138 3 0 0

1 E 97 Total C N O S802 506 155 138 3 0 0

• Molecule 2 is a protein called Histone H4.


2 B 82 Total C N O S657 416 128 112 1 0 0

2 F 81 Total C N O S648 410 126 111 1 0 0

• Molecule 3 is a protein called Histone H2A.


3 C 107 Total C N O823 519 161 143 0 0

3 G 104 Total C N O800 504 156 140 0 0

• Molecule 4 is a protein called Histone H2B 1.1.


4 D 92 Total C N O S718 451 128 136 3 0 0

4 H 94 Total C N O S733 460 131 139 3 0 0

There are 4 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceD 29 THR SER engineered mutation UNP P02281

Continued on next page...

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


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

D 117 CYS LYS engineered mutation UNP P02281H 29 THR SER engineered mutation UNP P02281H 117 CYS LYS engineered mutation UNP P02281

• Molecule 5 is a DNA chain called DNA (144-MER).


5 I 144 Total C N O P2935 1393 536 862 144 0 0

• Molecule 6 is a DNA chain called DNA (145-MER).


6 J 145 Total C N O P2990 1415 559 871 145 0 0

• Molecule 7 is a protein called Histone-lysine N-methyltransferase 2C.


7 K 156 Total C N O S1259 784 235 228 12 0 0

There is a discrepancy between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceK 4708 SER CYS engineered mutation UNP Q8NEZ4

• Molecule 8 is a protein called Retinoblastoma-binding protein 5.


8 N 347 Total C N O S2724 1715 472 522 15 0 0

• Molecule 9 is a protein called Ubiquitin.


9 O 76 Total C N O S603 379 105 117 2 0 0

There is a discrepancy between the modelled and reference sequences:


Chain Residue Modelled Actual Comment ReferenceO 76 CYS GLY engineered mutation UNP P62979

• Molecule 10 is a protein called WD repeat-containing protein 5.


10 R 300 Total C N O S2326 1485 388 444 9 0 0

• Molecule 11 is a protein called Set1/Ash2 histone methyltransferase complex subunit ASH2.


11 T 176 Total C N O S1404 907 235 256 6 0 0

• Molecule 12 is ZINC ION (three-letter code: ZN) (formula: Zn).

Mol Chain Residues Atoms AltConf

12 K 1 Total Zn1 1 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: Histone H3

Chain A:

ALA

ARG

THR

LYS

GLN

THR

ALA

ARG

LYS

SER

THR

GLY

GLY

LYS

ALA

PRO

ARG

LYS

GLN

LEU

ALA

THR

LYS

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ALA

ARG

LYS

SER

ALA

PRO

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THR

GLY

GLY

VAL

LYS

LYS

P38

E50

R53

S57

T58

R63

Q68

R72

R83

D106

T107

N108

R131

R134

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A


Chain E:

ALA

ARG

THR

LYS

GLN

THR

ALA

ARG

LYS

SER

THR

GLY

GLY

LYS

ALA

PRO

ARG

LYS

GLN

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ARG

LYS

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ALA

PRO

ALA

THR

GLY

GLY

VAL

LYS

LYS

P38

E50

R53

R63

Q68

R72

E73

Q76

D106

T107

N108

R131

R134

ALA


Chain B:

SER

GLY

ARG

GLY

LYS

GLY

GLY

LYS

GLY

LEU

GLY

LYS

GLY

GLY

ALA

LYS

ARG

HIS

ARG

K20

R40

G41

G42

S47

G48

N64

R67

T80

G101

GLY


Chain F:

SER

GLY

ARG

GLY

LYS

GLY

GLY

LYS

GLY

LEU

GLY

LYS

GLY

GLY

ALA

LYS

ARG

HIS

ARG

LYS

V21

N25

R39

G42

V43

K44

R45

G101

GLY

• Molecule 3: Histone H2A

Chain C:

SER

GLY

ARG

GLY

LYS

GLN

GLY

GLY

LYS

THR

ARG

A12

R32

K118

LYS

THR

GLU

SER

SER

LYS

SER

ALA

LYS

SER

LYS

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


• Molecule 3: Histone H2A

Chain G:

SER

GLY

ARG

GLY

LYS

GLN

GLY

GLY

LYS

THR

ARG

ALA

LYS

A14

P26

R29

R32

N110

P117

LYS

LYS

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SER

LYS

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ALA

LYS

SER

LYS

• Molecule 4: Histone H2B 1.1

Chain D:

ALA

LYS

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PRO

ALA

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LYS

LYS

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LYS

LYS

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LYS

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LYS

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ARG

LYS

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LYS

• Molecule 4: Histone H2B 1.1

Chain H:

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LYS

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LYS

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LYS

LYS

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VAL

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ASP

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ARG

ARG

LYS

T29

R30

K31

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• Molecule 5: DNA (144-MER)

Chain I:

C3 G4 C24

G25

G50

A60

A61

C81

A135

T136

A137

T138

A139

G145

A146

• Molecule 6: DNA (145-MER)

Chain J:

T2�

T15

G23

T24

C27

T28

G29

G30

A31

G32

A60

G82

T83

G95

T96

T99

C123

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• Molecule 7: Histone-lysine N-methyltransferase 2C

Chain K:

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• Molecule 8: Retinoblastoma-binding protein 5

Chain N:

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• Molecule 9: Ubiquitin

Chain O:

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• Molecule 10: WD repeat-containing protein 5

Chain R:

MET

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GLU

GLU

LYS

LYS

PRO

GLU

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GLU

ALA

ALA

ARG

ALA

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VAL

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• Molecule 11: Set1/Ash2 histone methyltransferase complex subunit ASH2

Chain T:

MET

ASP

THR

GLN

ALA

GLY

SER

VAL

ASP

GLU

GLU

ASN

GLY

ARG

GLN

LEU

GLY

GLU

VAL

GLU

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CYS

GLY

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CYS

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LYS

TRP

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CYS

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LYS

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LYS

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LYS

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ARG

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LYS

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4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C1 DepositorNumber of particles used 81945 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING ONLY DepositorMicroscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å2) 40.0 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector FEI FALCON III (4k x 4k) DepositorMaximum map value 0.166 DepositorMinimum map value -0.114 DepositorAverage map value 0.000 DepositorMap value standard deviation 0.006 DepositorRecommended contour level 0.015 DepositorMap size (Å) 294.30002, 294.30002, 294.30002 wwPDBMap dimensions 270, 270, 270 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.09, 1.09, 1.09 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

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 0/814 0.59 0/10921 E 0.36 0/814 0.59 0/10922 B 0.45 0/664 0.63 0/8892 F 0.45 0/655 0.59 0/8783 C 0.37 0/833 0.54 0/11243 G 0.35 0/810 0.55 0/10954 D 0.41 0/729 0.55 0/9834 H 0.37 0/744 0.55 0/10015 I 0.72 0/3289 1.00 1/5069 (0.0%)6 J 0.71 0/3357 0.98 0/51847 K 0.28 0/1281 0.53 0/17158 N 0.30 0/2781 0.56 0/37779 O 0.26 0/609 0.57 0/81910 R 0.27 0/2382 0.54 1/3231 (0.0%)11 T 0.28 0/1445 0.55 0/1954All All 0.48 0/21207 0.74 2/29903 (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 outliers8 N 0 1

There are no bond length outliers.

All (2) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 I 4 DG O4’-C4’-C3’ -6.81 101.78 104.50


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


Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)10 R 309 CYS C-N-CA 5.75 136.08 121.70

There are no chirality outliers.

All (1) planarity outliers are listed below:

Mol Chain Res Type Group8 N 327 GLU 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 802 0 841 8 01 E 802 0 841 7 02 B 657 0 706 6 02 F 648 0 693 5 03 C 823 0 882 1 03 G 800 0 851 2 04 D 718 0 734 3 04 H 733 0 752 3 05 I 2935 0 1615 9 06 J 2990 0 1628 10 07 K 1259 0 1252 22 08 N 2724 0 2677 35 09 O 603 0 631 11 010 R 2326 0 2309 48 011 T 1404 0 1369 24 012 K 1 0 0 0 0All All 20225 0 17781 163 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 4.

All (163) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

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


Atom-1 Atom-2 Interatomicdistance (Å)Clash

overlap (Å)1:E:63:ARG:HH21 6:J:60:DA:H5” 1.56 0.719:O:44:ILE:HB 9:O:68:HIS:HB2 1.78 0.65

1:E:76:GLN:HE22 2:F:21:VAL:HG23 1.62 0.648:N:27:ALA:H 8:N:316:GLY:HA2 1.61 0.63

11:T:315:MET:SD 11:T:317:ARG:NH1 2.73 0.6210:R:205:CYS:SG 10:R:206:LEU:N 2.73 0.6110:R:111:LEU:HB2 10:R:125:LEU:HB2 1.83 0.6110:R:283:VAL:HB 10:R:297:LEU:HB2 1.83 0.602:B:64:ASN:OD1 2:B:67:ARG:NH2 2.35 0.595:I:25:DG:H1 6:J:123:DC:H42 1.49 0.59

1:E:108:ASN:ND2 2:F:42:GLY:O 2.36 0.5910:R:267:SER:HB3 10:R:273:TRP:HB2 1.85 0.5910:R:90:ILE:HA 10:R:106:SER:HA 1.84 0.5811:T:325:GLY:H 11:T:398:LEU:HB2 1.67 0.58

10:R:230:LEU:HD23 10:R:264:ALA:HB1 1.84 0.581:E:106:ASP:OD2 1:E:131:ARG:NH2 2.36 0.581:A:106:ASP:OD2 1:A:131:ARG:NH2 2.36 0.5811:T:307:VAL:HG21 11:T:316:VAL:HG11 1.85 0.587:K:4783:LEU:HD11 8:N:329:TRP:HZ2 1.68 0.588:N:172:LYS:HB3 8:N:190:ARG:HH22 1.69 0.573:C:32:ARG:NH2 4:D:32:GLU:OE2 2.38 0.57

11:T:367:ARG:HH21 11:T:370:LYS:HB2 1.70 0.564:D:119:THR:HG21 8:N:246:GLN:HE21 1.71 0.5610:R:207:LYS:NZ 10:R:244:SER:O 2.39 0.561:A:108:ASN:ND2 2:B:42:GLY:O 2.39 0.5610:R:61:ALA:H 10:R:95:TRP:HH2 1.53 0.56

11:T:318:ALA:HB3 11:T:470:PRO:HD2 1.89 0.557:K:4818:GLU:O 10:R:214:ASN:ND2 2.39 0.55

7:K:4768:GLU:HB2 7:K:4771:SER:HB2 1.90 0.5411:T:464:PHE:O 11:T:468:TYR:OH 2.25 0.541:E:73:GLU:HB2 2:F:25:ASN:HD22 1.73 0.53

7:K:4854:ASN:ND2 7:K:4881:GLU:O 2.39 0.531:A:57:SER:O 2:B:40:ARG:NH2 2.41 0.53

9:O:39:ASP:HB2 9:O:74:ARG:HB3 1.89 0.539:O:33:LYS:HG3 9:O:34:GLU:HG2 1.90 0.5311:T:330:GLU:HA 11:T:393:GLY:HA2 1.91 0.537:K:4805:ILE:HG23 7:K:4809:VAL:HB 1.90 0.528:N:31:THR:HG23 8:N:74:TRP:HD1 1.73 0.5210:R:102:LEU:HB2 10:R:114:TRP:HB2 1.92 0.521:A:63:ARG:HH21 5:I:60:DA:H5” 1.74 0.5210:R:129:SER:OG 10:R:150:ASP:OD2 2.26 0.527:K:4710:ARG:HD2 10:R:49:SER:HB2 1.91 0.52



Continued from previous page...


overlap (Å)1:A:83:ARG:HB3 2:B:80:THR:HG22 1.93 0.51

10:R:233:THR:OG1 10:R:237:THR:O 2.28 0.517:K:4849:HIS:ND1 7:K:4884:TYR:O 2.40 0.517:K:4783:LEU:O 7:K:4848:ASN:ND2 2.43 0.513:G:32:ARG:NH2 4:H:32:GLU:OE2 2.44 0.51

10:R:295:GLN:HE21 10:R:297:LEU:HD21 1.76 0.502:F:39:ARG:NH1 2:F:44:LYS:O 2.41 0.502:F:45:ARG:HE 5:I:81:DC:H4’ 1.76 0.506:J:95:DG:H2’ 6:J:96:DT:H71 1.92 0.50

8:N:379:SER:OG 10:R:225:ASN:ND2 2.45 0.507:K:4860:VAL:HB 7:K:4869:ILE:HG13 1.94 0.498:N:178:LEU:HB3 8:N:183:GLN:HA 1.94 0.4911:T:347:SER:N 11:T:469:PHE:O 2.43 0.498:N:296:GLU:OE1 8:N:314:SER:OG 2.29 0.498:N:331:ALA:HB1 10:R:205:CYS:HB3 1.93 0.498:N:302:ALA:HB3 8:N:311:ALA:HB3 1.93 0.499:O:14:THR:O 9:O:33:LYS:NZ 2.37 0.49

10:R:209:LEU:HD11 10:R:241:TRP:HB3 1.93 0.4911:T:399:PRO:HD2 11:T:445:SER:HB3 1.94 0.497:K:4792:GLU:OE1 7:K:4875:ARG:NE 2.43 0.4910:R:232:ALA:HA 10:R:238:LEU:HD22 1.93 0.4811:T:332:THR:N 11:T:481:SER:O 2.45 0.48

7:K:4805:ILE:HD11 7:K:4836:ASP:HB2 1.95 0.487:K:4900:HIS:NE2 10:R:150:ASP:OD2 2.47 0.488:N:229:GLU:OE2 9:O:72:ARG:NH2 2.44 0.4810:R:278:SER:H 10:R:304:VAL:HB 1.78 0.48

8:N:217:THR:HG21 8:N:223:ARG:HH11 1.79 0.488:N:270:SER:OG 8:N:271:ALA:N 2.47 0.47

7:K:4820:GLN:HE21 10:R:212:ASP:HA 1.79 0.4711:T:298:LEU:HD13 11:T:316:VAL:HB 1.95 0.477:K:4841:GLY:HA2 8:N:339:LEU:HG 1.97 0.475:I:135:DA:H2’ 5:I:136:DT:H71 1.96 0.4710:R:186:ILE:O 10:R:198:TRP:N 2.40 0.46

11:T:357:LEU:HG 11:T:365:SER:HB3 1.97 0.464:H:30:ARG:HH12 6:J:29:DG:H5’ 1.80 0.466:J:82:DG:H2’ 6:J:83:DT:C6 2.50 0.4610:R:71:ILE:HB 10:R:80:GLU:HB3 1.98 0.46

11:T:330:GLU:HB2 11:T:483:ASN:HB3 1.96 0.4611:T:311:LYS:HG2 11:T:476:LYS:HG2 1.97 0.467:K:4800:TYR:CZ 7:K:4827:PHE:HB3 2.50 0.468:N:217:THR:OG1 8:N:221:ILE:O 2.28 0.46





overlap (Å)7:K:4759:SER:HB3 7:K:4763:ARG:HH12 1.81 0.467:K:4791:ILE:O 7:K:4876:ILE:N 2.49 0.468:N:264:GLU:O 8:N:281:LYS:N 2.49 0.46

8:N:377:VAL:HG23 10:R:228:TYR:HB2 1.98 0.4610:R:286:TRP:HD1 10:R:294:VAL:HG22 1.81 0.468:N:313:ILE:HG12 8:N:318:VAL:HG22 1.98 0.4510:R:186:ILE:HB 10:R:198:TRP:HB2 1.99 0.457:K:4803:THR:HB 7:K:4836:ASP:HB3 1.98 0.458:N:56:ARG:O 10:R:162:LYS:NZ 2.44 0.45

8:N:282:SER:HB2 9:O:73:LEU:HD22 1.97 0.459:O:27:LYS:HB3 9:O:38:PRO:HB3 1.98 0.45

10:R:157:ASP:HB3 10:R:161:GLY:H 1.82 0.4510:R:279:GLU:HG2 10:R:303:VAL:HG13 1.97 0.4510:R:41:LEU:HB2 10:R:327:ILE:HB 1.99 0.4511:T:288:LEU:O 11:T:319:SER:OG 2.32 0.4510:R:278:SER:OG 10:R:279:GLU:N 2.49 0.458:N:307:ARG:NH1 10:R:201:ALA:O 2.50 0.457:K:4777:ARG:NH1 10:R:166:THR:O 2.49 0.45

6:J:15:DT:H6 6:J:15:DT:H2’ 1.65 0.448:N:152:ASP:HB3 8:N:171:ALA:HB3 1.99 0.44

5:I:50:DG:N2 6:J:99:DT:O2 2.50 0.4411:T:322:VAL:HG21 11:T:327:TRP:CD1 2.51 0.44

8:N:90:VAL:HB 8:N:104:PHE:HB2 1.99 0.448:N:166:ILE:HG13 8:N:180:THR:HA 1.98 0.448:N:298:LEU:HA 8:N:314:SER:HB3 1.98 0.4410:R:189:SER:HB3 10:R:220:VAL:HG22 1.99 0.448:N:160:ASP:OD1 8:N:164:GLU:N 2.49 0.4411:T:347:SER:O 11:T:469:PHE:N 2.51 0.4410:R:175:SER:OG 10:R:189:SER:OG 2.27 0.443:G:26:PRO:HG3 3:G:29:ARG:HD3 2.00 0.4310:R:154:ARG:NH1 10:R:163:CYS:SG 2.91 0.435:I:138:DT:H2” 5:I:139:DA:C8 2.53 0.43

10:R:170:HIS:HD2 10:R:174:VAL:HG22 1.83 0.4310:R:190:SER:OG 10:R:191:TYR:N 2.51 0.438:N:371:GLU:N 10:R:249:LEU:O 2.51 0.43

11:T:301:SER:OG 11:T:306:THR:O 2.37 0.438:N:70:CYS:SG 8:N:71:SER:N 2.91 0.4311:T:358:GLY:O 11:T:377:SER:N 2.52 0.435:I:145:DG:H2” 5:I:146:DA:C8 2.54 0.439:O:1:MET:HB3 9:O:17:VAL:HG23 2.01 0.436:J:23:DG:H2” 6:J:24:DT:H5’ 2.02 0.42





overlap (Å)9:O:40:GLN:O 9:O:42:ARG:N 2.53 0.421:A:50:GLU:HA 1:A:53:ARG:HB3 2.01 0.428:N:114:GLN:O 8:N:124:LEU:N 2.48 0.42

1:E:68:GLN:HE21 1:E:72:ARG:HH21 1.68 0.426:J:31:DA:H2’ 6:J:32:DG:C8 2.55 0.42

8:N:220:ARG:HG2 8:N:253:PRO:HA 2.02 0.424:H:119:THR:HA 4:H:122:LYS:HB2 2.02 0.428:N:80:LYS:HD2 8:N:92:GLN:HE21 1.84 0.42

11:T:348:GLN:HB2 11:T:362:PHE:HB3 2.02 0.4211:T:335:GLU:HA 11:T:388:GLN:HG3 2.02 0.428:N:136:THR:OG1 8:N:139:ASP:O 2.37 0.411:A:68:GLN:HE21 1:A:72:ARG:HH21 1.68 0.418:N:300:ASP:HB3 8:N:313:ILE:HD12 2.02 0.41

9:O:6:LYS:N 9:O:67:LEU:O 2.43 0.415:I:60:DA:H2” 5:I:61:DA:C8 2.56 0.41

10:R:178:HIS:HB3 10:R:187:VAL:HG12 2.02 0.4110:R:217:VAL:HA 10:R:232:ALA:HB3 2.03 0.41

10:R:209:LEU:HD21 10:R:241:TRP:CD2 2.56 0.4110:R:306:SER:HB3 10:R:319:ALA:HB3 2.03 0.417:K:4899:CYS:SG 7:K:4900:HIS:N 2.94 0.419:O:30:ILE:HA 9:O:33:LYS:HG2 2.03 0.41

11:T:287:VAL:HG13 11:T:320:HIS:HB2 2.03 0.4111:T:343:ARG:HB3 11:T:365:SER:HB2 2.02 0.412:B:47:SER:OG 2:B:48:GLY:N 2.53 0.411:E:50:GLU:HA 1:E:53:ARG:HB3 2.02 0.41

10:R:282:LEU:HD13 10:R:296:LYS:HD2 2.03 0.415:I:24:DC:H2” 5:I:25:DG:C8 2.56 0.41

7:K:4849:HIS:CE1 7:K:4885:ASP:HA 2.56 0.4110:R:42:ALA:HB2 10:R:326:THR:HG22 2.02 0.4110:R:35:TYR:HD2 10:R:295:GLN:HE22 1.69 0.401:A:58:THR:HA 2:B:40:ARG:HH22 1.87 0.4010:R:148:SER:OG 10:R:149:PHE:N 2.55 0.4010:R:191:TYR:HA 10:R:216:PRO:HA 2.01 0.404:D:95:VAL:HG13 4:D:99:LEU:HD12 2.04 0.408:N:348:ARG:NH2 8:N:350:SER:OG 2.54 0.4011:T:301:SER:OG 11:T:303:ASP:OD1 2.34 0.406:J:27:DC:H2” 6:J:28:DT:C5 2.57 0.40

7:K:4800:TYR:HB3 7:K:4868:ILE:HB 2.03 0.408:N:276:LEU:HB2 8:N:290:LEU:HB2 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 95/135 (70%) 89 (94%) 6 (6%) 0 100 100

1 E 95/135 (70%) 89 (94%) 6 (6%) 0 100 100

2 B 80/102 (78%) 73 (91%) 7 (9%) 0 100 100

2 F 79/102 (78%) 77 (98%) 2 (2%) 0 100 100

3 C 105/129 (81%) 99 (94%) 6 (6%) 0 100 100

3 G 102/129 (79%) 96 (94%) 6 (6%) 0 100 100

4 D 90/122 (74%) 88 (98%) 2 (2%) 0 100 100

4 H 92/122 (75%) 89 (97%) 3 (3%) 0 100 100

7 K 150/205 (73%) 132 (88%) 18 (12%) 0 100 100

8 N 343/538 (64%) 294 (86%) 49 (14%) 0 100 100

9 O 74/76 (97%) 68 (92%) 6 (8%) 0 100 100

10 R 298/334 (89%) 263 (88%) 35 (12%) 0 100 100

11 T 172/534 (32%) 157 (91%) 15 (9%) 0 100 100

All All 1775/2663 (67%) 1614 (91%) 161 (9%) 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 85/110 (77%) 84 (99%) 1 (1%) 71 84Continued on next page...

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


Continued from previous page...Mol Chain Analysed Rotameric Outliers Percentiles

1 E 85/110 (77%) 84 (99%) 1 (1%) 71 84

2 B 68/78 (87%) 68 (100%) 0 100 100

2 F 67/78 (86%) 67 (100%) 0 100 100

3 C 84/101 (83%) 84 (100%) 0 100 100

3 G 82/101 (81%) 81 (99%) 1 (1%) 71 84

4 D 79/102 (78%) 79 (100%) 0 100 100

4 H 80/102 (78%) 80 (100%) 0 100 100

7 K 136/182 (75%) 136 (100%) 0 100 100

8 N 304/462 (66%) 299 (98%) 5 (2%) 62 79

9 O 69/69 (100%) 69 (100%) 0 100 100

10 R 262/291 (90%) 262 (100%) 0 100 100

11 T 150/460 (33%) 150 (100%) 0 100 100

All All 1551/2246 (69%) 1543 (100%) 8 (0%) 89 93

All (8) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 53 ARG1 E 53 ARG3 G 110 ASN8 N 34 ARG8 N 250 ASN8 N 294 ARG8 N 324 ASN8 N 348 ARG

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (15)such sidechains are listed below:

Mol Chain Res Type1 A 68 GLN4 D 81 ASN1 E 76 GLN2 F 25 ASN3 G 110 ASN4 H 81 ASN7 K 4794 HIS7 K 4807 ASN



Continued from previous page...Mol Chain Res Type8 N 246 GLN8 N 273 GLN8 N 324 ASN8 N 328 ASN10 R 44 HIS10 R 136 ASN10 R 295 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 monosaccharides in this entry.

5.6 Ligand geometry i○

Of 1 ligands modelled in this entry, 1 is monoatomic - leaving 0 for Mogul analysis.

There are no bond length outliers.

There are no bond angle outliers.

There are no chirality outliers.

There are no torsion outliers.

There are no ring outliers.

No monomer is involved in short contacts.

5.7 Other polymers i○

There are no such residues in this entry.

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


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-0693. 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: 135 Y Index: 135 Z Index: 135

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: 153 Y Index: 120 Z Index: 142

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 0.015.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 shows the 3D surface view of the primary map at 50% transparency overlaid with thespecified mask at 0% transparency

A mask typically either:

• Encompasses the whole structure

• Separates out a domain, a functional unit, a monomer or an area of interest from a largerstructure

6.5.1 emd_0693_msk_1.map i○

X Y Z

https://www.wwpdb.org/validation/2017/EMValidationReportHelp#maskshttps://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 258 nm3; this corresponds to an approximatemass of 233 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 0.250 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 0.250 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 4.00 - -

Author-provided FSC curve 4.07 4.61 4.11Calculated* - - -

*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-0693 and PDBmodel 6KIW. Per-residue inclusion information can be found in section 3 on page 7.

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 0.015at 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, 81% of all backbone atoms, 78% 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 visualisationemd_0693_msk_1.map

Map analysisMap-value distributionVolume estimateRotationally averaged power spectrum

Fourier-Shell correlationFSCResolution estimates

Map-model fitMap-model overlayAtom inclusion

full wwpdb em map/model validation report o i · 2020. 8. 30. · page 4 ullf wwpdb em map/model...

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