full wwpdb em validation report i - rcsbfull wwpdb em validation report i dec13,2020–05:16pmest...

Full wwPDB EM Validation Report i○

Dec 13, 2020 – 05:16 PM EST

PDB ID : 6D6VEMDB ID : EMD-7821

Title : CryoEM structure of Tetrahymena telomerase with telomeric DNA at 4.8Angstrom resolution

Authors : Jiang, J.; Wang, Y.; Susac, L.; Chan, H.; Basu, R.; Zhou, Z.H.; Feigon, J.Deposited on : 2018-04-22

Resolution : 4.80 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/EMValidationReportHelp



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

Full wwPDB EM Validation Report EMD-7821, 6D6V

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 4.80 Å.

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

Metric Whole archive(#Entries)

EM structures(#Entries)

Clashscore 158937 4297Ramachandran outliers 154571 4023

Sidechain outliers 154315 3826RNA backbone 4643 859

The table below summarises the geometric issues observed across the polymeric chains and their fitto the map. The red, orange, yellow and green segments of the bar indicate the fraction of residuesthat contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria respectively. A greysegment represents the fraction of residues that are not modelled. The numeric value for eachfraction is indicated below the corresponding segment, with a dot representing fractions <=5%The upper red bar (where present) indicates the fraction of residues that have poor fit to the EMmap (all-atom inclusion < 40%). The numeric value is given above the bar.

Mol Chain Length Quality of chain

1 A 1117

2 D 701

3 F 121

4 E 269

5 B 159

6 C 19

7 G 157Continued on next page...

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


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

8 H 542


2 Entry composition i○

There are 9 unique types of molecules in this entry. The entry contains 17317 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 Telomerase reverse transcriptase.

Mol Chain Residues Atoms AltConf Trace

1 A 980 Total C N O S8253 5357 1369 1498 29 0 0

• Molecule 2 is a protein called Telomerase-associated protein 82.


2 D 185 Total C N O S1538 985 255 290 8 0 0

• Molecule 3 is a protein called Telomerase holoenzyme TEB heterotrimer Teb3 subunit.


3 F 113 Total C N O S919 580 155 180 4 0 0

• Molecule 4 is a protein called Telomerase holoenzyme Teb2 subunit.


4 E 149 Total C N O S1207 765 211 223 8 0 0

• Molecule 5 is a RNA chain called RNA (159-MER).


5 B 159 Total C N O P3322 1494 568 1102 158 0 0

• Molecule 6 is a DNA chain called DNA (5’-D(P*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*G)-3’).


6 C 19 Total C N O P406 190 77 120 19 0 0

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


• Molecule 7 is a protein called Telomerase-associated protein 50.


7 G 157 Total C N O785 471 157 157 0 0

• Molecule 8 is a protein called Telomerase associated protein p65.


8 H 108 Total C N O S886 563 156 162 5 0 0

• Molecule 9 is ZINC ION (three-letter code: ZN) (formula: Zn).

Mol Chain Residues Atoms AltConf

9 D 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: Telomerase reverse transcriptase

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


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• Molecule 2: Telomerase-associated protein 82

Chain D:

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• Molecule 3: Telomerase holoenzyme TEB heterotrimer Teb3 subunit

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• Molecule 4: Telomerase holoenzyme Teb2 subunit

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• Molecule 5: RNA (159-MER)

Chain B:


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• Molecule 6: DNA (5’-D(P*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*GP*GP*GP*G)-3’)

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• Molecule 7: Telomerase-associated protein 50

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• Molecule 8: Telomerase associated protein p65

Chain H:

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4 Experimental information i○

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, Not providedNumber of particles used 52506 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

) 52 DepositorMinimum defocus (nm) Not providedMaximum defocus (nm) Not providedMagnification Not providedImage detector GATAN K2 QUANTUM (4k x 4k) DepositorMaximum map value 0.156 DepositorMinimum map value -0.054 DepositorAverage map value -0.000 DepositorMap value standard deviation 0.006 DepositorRecommended contour level 0.055 DepositorMap size (Å) 348.16, 348.16, 348.16 wwPDBMap dimensions 256, 256, 256 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.36, 1.36, 1.36 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| >5

1 A 0.73 1/8418 (0.0%) 0.89 16/11318 (0.1%)2 D 0.69 0/1566 0.77 1/2101 (0.0%)3 F 0.59 0/934 0.73 0/12624 E 0.64 0/1230 0.82 1/1655 (0.1%)5 B 1.13 9/3711 (0.2%) 2.03 208/5768 (3.6%)6 C 1.56 2/456 (0.4%) 1.49 10/707 (1.4%)8 H 0.31 1/899 (0.1%) 0.35 0/1205All All 0.84 13/17214 (0.1%) 1.25 236/24016 (1.0%)

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 0 253 F 0 44 E 0 57 G 0 6All All 0 40

All (13) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)5 B 44 A N9-C4 -6.88 1.33 1.376 C 9 DT C3’-O3’ 6.75 1.52 1.445 B 33 A N9-C4 -6.42 1.33 1.375 B 47 C N1-C6 -6.41 1.33 1.375 B 69 A N9-C4 -6.27 1.34 1.376 C 15 DT C3’-O3’ -5.76 1.36 1.448 H 527 MET CG-SD 5.68 1.96 1.81

Continued on next page...

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

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


Continued from previous page...Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)5 B 22 A N9-C4 -5.67 1.34 1.375 B 49 C C4-C5 -5.61 1.38 1.435 B 49 C C5-C6 -5.52 1.29 1.345 B 29 A N9-C4 5.49 1.41 1.371 A 120 GLU CB-CG 5.37 1.62 1.525 B 148 A N7-C5 -5.10 1.36 1.39

All (236) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 B 46 C O4’-C1’-N1 22.24 125.99 108.205 B 47 C C5-C6-N1 16.33 129.16 121.005 B 47 C C6-N1-C2 -14.86 114.36 120.305 B 48 C C5-C6-N1 14.04 128.02 121.005 B 145 U N1-C2-O2 13.35 132.15 122.805 B 49 C C2-N1-C1’ 13.19 133.30 118.805 B 25 U C2-N1-C1’ 12.88 133.15 117.705 B 120 C N1-C2-O2 12.79 126.57 118.905 B 145 U N3-C2-O2 -12.34 113.56 122.205 B 17 U N3-C2-O2 -12.03 113.78 122.205 B 49 C C5-C4-N4 -11.96 111.82 120.205 B 145 U C2-N1-C1’ 11.82 131.88 117.705 B 53 A O5’-P-OP2 -11.63 95.24 105.705 B 48 C C6-N1-C2 -11.54 115.68 120.305 B 49 C C5-C6-N1 11.23 126.62 121.005 B 25 U N1-C2-O2 10.72 130.31 122.805 B 123 C N1-C2-O2 10.68 125.31 118.905 B 17 U N1-C2-O2 10.61 130.22 122.805 B 49 C C6-N1-C1’ -10.52 108.17 120.805 B 112 A N1-C6-N6 10.43 124.86 118.605 B 120 C N3-C2-O2 -9.73 115.09 121.905 B 82 U N3-C2-O2 -9.71 115.40 122.205 B 102 U C5-C6-N1 9.36 127.38 122.705 B 145 U C6-N1-C1’ -9.30 108.18 121.205 B 25 U C6-N1-C1’ -9.21 108.31 121.205 B 35 C N1-C2-O2 9.20 124.42 118.906 C 14 DT O4’-C1’-N1 9.20 114.44 108.005 B 148 A C6-C5-N7 -9.12 125.91 132.305 B 70 A N9-C4-C5 -9.03 102.19 105.805 B 152 C C5-C6-N1 9.01 125.50 121.005 B 88 C N3-C4-C5 8.85 125.44 121.905 B 123 C N3-C2-O2 -8.72 115.79 121.90



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 B 49 C N3-C4-N4 8.70 124.09 118.005 B 81 U N3-C2-O2 -8.64 116.15 122.205 B 33 A O4’-C1’-N9 8.58 115.06 108.205 B 120 C C2-N1-C1’ 8.56 128.22 118.805 B 25 U N3-C2-O2 -8.51 116.24 122.205 B 137 U N1-C2-O2 8.47 128.73 122.805 B 137 U C2-N1-C1’ 8.41 127.80 117.705 B 82 U N1-C2-O2 8.22 128.56 122.805 B 84 G N7-C8-N9 8.08 117.14 113.101 A 651 LEU CA-CB-CG 8.06 133.84 115.305 B 3 A P-O3’-C3’ 8.04 129.34 119.705 B 69 A N3-C4-N9 -7.96 121.03 127.405 B 85 G N7-C8-N9 7.90 117.05 113.105 B 52 A C2-N3-C4 7.89 114.54 110.605 B 118 A O5’-P-OP1 -7.83 98.65 105.701 A 830 LEU CA-CB-CG 7.78 133.19 115.305 B 103 G C4-C5-N7 7.75 113.90 110.805 B 35 C N3-C2-O2 -7.73 116.49 121.905 B 150 G N7-C8-N9 7.71 116.95 113.105 B 49 C N1-C2-O2 7.67 123.50 118.905 B 33 A C8-N9-C1’ 7.66 141.49 127.705 B 6 C C5-C6-N1 7.65 124.82 121.005 B 17 U C2-N1-C1’ 7.55 126.76 117.705 B 81 U N1-C2-O2 7.53 128.07 122.805 B 8 C C5-C6-N1 7.51 124.76 121.005 B 137 U N3-C2-O2 -7.46 116.98 122.205 B 69 A C6-C5-N7 7.43 137.50 132.305 B 52 A N3-C4-N9 7.34 133.28 127.405 B 33 A C4-N9-C1’ -7.30 113.17 126.305 B 47 C O4’-C1’-N1 7.23 113.98 108.205 B 114 G C4-C5-N7 7.20 113.68 110.805 B 57 U C2-N1-C1’ 7.15 126.28 117.705 B 57 U N1-C2-O2 7.13 127.79 122.805 B 120 C C6-N1-C1’ -7.12 112.26 120.805 B 48 C C4-C5-C6 -7.09 113.86 117.405 B 148 A C4-C5-N7 7.04 114.22 110.705 B 46 C P-O5’-C5’ 7.02 132.14 120.905 B 112 A C5-C6-N6 -7.01 118.09 123.705 B 112 A C4-C5-N7 6.99 114.19 110.705 B 69 A N1-C2-N3 6.97 132.78 129.305 B 96 U N3-C2-O2 -6.96 117.32 122.205 B 84 G C5-N7-C8 -6.96 100.82 104.30



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 B 70 A C4-C5-N7 6.89 114.14 110.705 B 103 G C5-N7-C8 -6.88 100.86 104.301 A 922 SER C-N-CA 6.79 138.67 121.705 B 62 C N3-C2-O2 -6.78 117.16 121.905 B 49 C C4-C5-C6 -6.74 114.03 117.405 B 33 A N3-C4-N9 -6.73 122.02 127.405 B 123 C C5-C6-N1 6.71 124.35 121.005 B 85 G C5-N7-C8 -6.67 100.97 104.305 B 95 G N3-C4-N9 6.66 130.00 126.006 C 1 DG P-O3’-C3’ 6.65 127.67 119.705 B 114 G C5-N7-C8 -6.60 101.00 104.305 B 53 A N9-C4-C5 6.60 108.44 105.805 B 69 A C4-N9-C1’ -6.59 114.43 126.305 B 73 U N3-C2-O2 -6.59 117.58 122.205 B 73 U N1-C2-O2 6.57 127.40 122.805 B 47 C N3-C4-N4 6.57 122.60 118.005 B 88 C C6-N1-C2 6.57 122.93 120.305 B 18 U N1-C2-O2 6.56 127.39 122.805 B 69 A C2-N3-C4 -6.56 107.32 110.605 B 8 C N1-C2-O2 6.54 122.83 118.905 B 70 A N1-C6-N6 6.54 122.52 118.605 B 80 A N1-C2-N3 -6.51 126.05 129.305 B 134 C N1-C2-O2 6.51 122.80 118.905 B 150 G C5-N7-C8 -6.45 101.08 104.305 B 148 A N9-C4-C5 -6.45 103.22 105.805 B 25 U C5-C6-N1 6.40 125.90 122.705 B 83 A N7-C8-N9 6.37 116.98 113.805 B 47 C C2-N3-C4 6.35 123.08 119.905 B 54 A O5’-P-OP1 -6.34 100.00 105.705 B 148 A N1-C6-N6 6.27 122.36 118.605 B 148 A N7-C8-N9 6.27 116.94 113.805 B 57 U C6-N1-C1’ -6.26 112.43 121.205 B 41 U OP1-P-O3’ 6.19 118.82 105.205 B 8 C C2-N1-C1’ 6.16 125.58 118.805 B 42 U C6-N1-C2 -6.15 117.31 121.005 B 77 C N1-C2-O2 6.13 122.58 118.905 B 69 A C8-N9-C1’ 6.11 138.70 127.705 B 29 A C2-N3-C4 6.10 113.65 110.605 B 123 C C6-N1-C2 -6.07 117.87 120.305 B 69 A C4-C5-C6 -6.05 113.98 117.005 B 152 C C4-C5-C6 -6.04 114.38 117.406 C 1 DG OP2-P-O3’ 5.99 118.38 105.20



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 B 62 C N1-C2-O2 5.98 122.49 118.905 B 137 U C6-N1-C1’ -5.97 112.83 121.201 A 989 LEU CA-CB-CG -5.95 101.62 115.305 B 73 U C5-C6-N1 5.93 125.67 122.705 B 103 G N7-C8-N9 5.88 116.04 113.105 B 111 A C6-N1-C2 5.88 122.13 118.605 B 69 A N3-C4-C5 5.86 130.90 126.805 B 94 A N1-C2-N3 -5.86 126.37 129.305 B 114 G N1-C6-O6 5.86 123.41 119.905 B 46 C C6-N1-C2 5.85 122.64 120.305 B 20 A N9-C4-C5 -5.83 103.47 105.805 B 77 C C5-C6-N1 5.82 123.91 121.005 B 124 A C8-N9-C4 -5.81 103.47 105.805 B 42 U C5-C6-N1 5.79 125.60 122.705 B 112 A C5-N7-C8 -5.77 101.02 103.905 B 36 U N3-C2-O2 -5.75 118.17 122.205 B 112 A N9-C4-C5 -5.75 103.50 105.806 C 14 DT C1’-O4’-C4’ -5.74 104.36 110.106 C 9 DT P-O3’-C3’ 5.73 126.58 119.705 B 33 A P-O3’-C3’ 5.72 126.57 119.701 A 507 LEU CA-CB-CG 5.71 128.44 115.306 C 2 DT O4’-C4’-C3’ -5.70 102.22 104.505 B 8 C C6-N1-C2 -5.69 118.02 120.305 B 46 C C1’-O4’-C4’ -5.69 105.35 109.905 B 29 A N3-C4-N9 5.68 131.95 127.401 A 731 VAL CG1-CB-CG2 -5.67 101.82 110.905 B 114 G N7-C8-N9 5.66 115.93 113.105 B 103 G N1-C6-O6 5.65 123.29 119.902 D 646 LEU CA-CB-CG -5.65 102.31 115.305 B 148 A C4-C5-C6 5.64 119.82 117.005 B 69 A N9-C4-C5 5.64 108.06 105.801 A 1050 LEU CA-CB-CG -5.63 102.34 115.305 B 96 U C6-N1-C2 -5.63 117.62 121.005 B 148 A N3-C4-N9 5.61 131.89 127.405 B 136 A P-O3’-C3’ 5.61 126.43 119.701 A 703 ILE CG1-CB-CG2 -5.60 99.08 111.405 B 22 A N3-C4-N9 -5.60 122.92 127.401 A 658 ARG NE-CZ-NH2 -5.59 117.51 120.304 E 140 ALA N-CA-CB -5.57 102.30 110.105 B 83 A C8-N9-C4 -5.57 103.57 105.805 B 20 A N1-C2-N3 -5.56 126.52 129.305 B 77 C C6-N1-C2 -5.55 118.08 120.30



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 B 137 U P-O3’-C3’ 5.53 126.33 119.705 B 148 A C5-N7-C8 -5.53 101.14 103.905 B 52 A N9-C4-C5 -5.52 103.59 105.805 B 29 A C4-N9-C1’ 5.51 136.22 126.301 A 627 ASP N-CA-C -5.50 96.14 111.006 C 7 DG O4’-C1’-N9 5.50 111.85 108.001 A 707 LEU CA-CB-CG 5.49 127.93 115.305 B 20 A C4-C5-N7 5.49 113.45 110.705 B 136 A OP2-P-O3’ 5.47 117.24 105.205 B 113 A N7-C8-N9 5.47 116.54 113.805 B 60 U P-O3’-C3’ 5.47 126.26 119.705 B 86 U N3-C2-O2 -5.47 118.37 122.205 B 22 A C2-N3-C4 -5.46 107.87 110.605 B 47 C N3-C4-C5 -5.45 119.72 121.901 A 570 LEU CA-CB-CG -5.45 102.76 115.305 B 88 C O4’-C1’-N1 5.45 112.56 108.205 B 9 U N1-C2-O2 5.43 126.60 122.805 B 42 U O4’-C1’-N1 5.43 112.54 108.205 B 9 U C5-C6-N1 5.42 125.41 122.705 B 47 C C4-C5-C6 -5.42 114.69 117.405 B 152 C C5-C4-N4 -5.40 116.42 120.205 B 49 C N3-C4-C5 5.40 124.06 121.905 B 57 U N3-C2-O2 -5.40 118.42 122.205 B 33 A C4-C5-C6 -5.39 114.30 117.005 B 59 G P-O3’-C3’ 5.38 126.16 119.705 B 95 G C8-N9-C1’ -5.38 120.00 127.005 B 33 A N3-C4-C5 5.38 130.57 126.805 B 75 C N1-C2-O2 5.37 122.12 118.905 B 58 A O4’-C1’-N9 5.37 112.50 108.201 A 585 TYR CA-CB-CG 5.35 123.56 113.405 B 112 A C6-C5-N7 -5.34 128.56 132.305 B 113 A N1-C6-N6 5.34 121.80 118.605 B 29 A N7-C8-N9 5.30 116.45 113.805 B 53 A N3-C4-N9 -5.30 123.16 127.405 B 44 A C2-N3-C4 -5.30 107.95 110.601 A 590 ASN C-N-CA 5.30 134.94 121.705 B 78 C C5-C6-N1 5.29 123.65 121.005 B 103 G C6-C5-N7 -5.29 127.22 130.405 B 152 C C6-N1-C2 -5.29 118.18 120.305 B 114 G C6-C5-N7 -5.29 127.23 130.405 B 70 A C5-N7-C8 -5.29 101.26 103.905 B 59 G N3-C4-N9 5.28 129.17 126.00



Continued from previous page...Mol Chain Res Type Atoms Z Observed(o) Ideal(o)5 B 85 G C6-C5-N7 -5.28 127.23 130.405 B 85 G C4-C5-N7 5.28 112.91 110.805 B 52 A N3-C4-C5 -5.27 123.11 126.805 B 49 C C6-N1-C2 -5.26 118.20 120.305 B 42 U C6-N1-C1’ 5.25 128.54 121.205 B 66 U O5’-P-OP1 -5.23 100.99 105.705 B 29 A N3-C4-C5 -5.18 123.17 126.806 C 11 DG OP2-P-O3’ 5.18 116.60 105.206 C 15 DT N3-C4-O4 5.18 123.01 119.905 B 18 U N3-C2-O2 -5.17 118.58 122.201 A 593 ILE CG1-CB-CG2 -5.17 100.02 111.405 B 41 U P-O3’-C3’ 5.17 125.90 119.705 B 138 U O4’-C1’-N1 5.16 112.33 108.205 B 80 A C6-N1-C2 5.15 121.69 118.605 B 84 G C4-C5-N7 5.14 112.86 110.805 B 52 A N1-C2-N3 -5.14 126.73 129.305 B 44 A N3-C4-N9 -5.12 123.30 127.405 B 132 C C2-N1-C1’ 5.12 124.43 118.805 B 69 A N1-C6-N6 -5.12 115.53 118.605 B 124 A N7-C8-N9 5.11 116.36 113.805 B 73 U C2-N1-C1’ 5.11 123.83 117.706 C 10 DG P-O3’-C3’ 5.10 125.81 119.705 B 6 C C2-N3-C4 5.08 122.44 119.901 A 20 LEU CA-CB-CG -5.07 103.64 115.305 B 62 C O4’-C1’-N1 5.07 112.25 108.205 B 129 A N9-C4-C5 -5.07 103.77 105.805 B 37 G N3-C4-C5 5.06 131.13 128.605 B 84 G C6-C5-N7 -5.04 127.38 130.405 B 24 C N1-C2-O2 5.03 121.92 118.905 B 53 A C8-N9-C1’ 5.02 136.74 127.705 B 83 A C5-N7-C8 -5.02 101.39 103.905 B 29 A C8-N9-C4 -5.02 103.79 105.805 B 62 C OP2-P-O3’ 5.02 116.24 105.205 B 44 A N3-C4-C5 5.01 130.31 126.805 B 20 A C5-C6-N1 5.01 120.20 117.705 B 42 U C2’-C3’-O3’ 5.00 121.70 113.70

There are no chirality outliers.

All (40) planarity outliers are listed below:

Mol Chain Res Type Group1 A 1004 LEU Peptide



Continued from previous page...Mol Chain Res Type Group1 A 1007 LEU Peptide1 A 122 GLU Peptide1 A 144 GLY Peptide1 A 17 LYS Peptide1 A 217 ASN Peptide1 A 233 ASN Peptide1 A 238 GLU Peptide1 A 240 GLY Peptide1 A 299 SER Peptide1 A 300 CYS Peptide1 A 548 PHE Peptide1 A 584 GLY Peptide1 A 698 LEU Peptide1 A 724 SER Peptide1 A 725 ASP Peptide1 A 760 PHE Peptide1 A 805 GLY Peptide1 A 84 PHE Peptide1 A 851 THR Peptide1 A 853 ASN Peptide1 A 865 HIS Peptide1 A 924 PHE Peptide1 A 933 ASN Peptide1 A 936 ILE Peptide4 E 122 ASN Peptide4 E 123 ASN Peptide4 E 125 ASN Peptide4 E 61 TYR Peptide4 E 81 ASP Peptide3 F 21 PHE Peptide3 F 58 ASN Peptide3 F 65 ASN Peptide3 F 97 PHE Peptide7 G 108 UNK Peptide7 G 109 UNK Peptide7 G 110 UNK Peptide7 G 136 UNK Peptide7 G 62 UNK Peptide7 G 66 UNK 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 8253 0 8327 437 02 D 1538 0 1524 76 03 F 919 0 898 36 04 E 1207 0 1198 75 05 B 3322 0 1686 140 06 C 406 0 216 16 07 G 785 0 177 42 08 H 886 0 880 73 09 D 1 0 0 0 0All All 17317 0 14906 795 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 26.

All (795) close contacts within the same asymmetric unit are listed below, sorted by their clashmagnitude.

Atom-1 Atom-2 Interatomicdistance (Å)

Clashoverlap (Å)

7:G:98:UNK:HA 7:G:123:UNK:CB 1.28 1.601:A:530:GLN:HG2 1:A:757:VAL:CG1 1.13 1.597:G:75:UNK:HA 7:G:110:UNK:CB 1.37 1.547:G:51:UNK:CB 7:G:73:UNK:O 1.64 1.457:G:50:UNK:O 7:G:74:UNK:CB 1.69 1.388:H:412:ASP:C 8:H:460:GLY:HA3 1.46 1.357:G:51:UNK:HA 7:G:74:UNK:CB 1.57 1.331:A:530:GLN:CG 1:A:757:VAL:CG1 2.07 1.324:E:140:ALA:O 4:E:141:GLN:HG2 1.28 1.315:B:122:A:N7 8:H:518:LYS:HD2 1.45 1.295:B:121:G:P 8:H:518:LYS:HA 1.72 1.27

7:G:51:UNK:CA 7:G:74:UNK:CB 2.19 1.215:B:140:A:H5’ 8:H:396:VAL:CG1 1.74 1.167:G:50:UNK:C 7:G:74:UNK:CB 2.24 1.157:G:98:UNK:CA 7:G:123:UNK:CB 2.24 1.157:G:75:UNK:CA 7:G:110:UNK:CB 2.23 1.155:B:121:G:OP1 8:H:518:LYS:HA 1.45 1.141:A:626:ILE:CG1 1:A:770:GLY:HA2 1.76 1.14


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


Continued from previous page...


Clashoverlap (Å)

5:B:122:A:N7 8:H:518:LYS:CD 2.10 1.145:B:122:A:C8 8:H:518:LYS:HG2 1.85 1.11

4:E:135:LYS:HE2 4:E:137:ARG:HD3 1.22 1.114:E:65:GLU:OE2 4:E:136:MET:O 1.67 1.104:E:46:ALA:HB1 4:E:138:LYS:HE3 1.31 1.105:B:140:A:C5’ 8:H:396:VAL:HG11 1.81 1.104:E:140:ALA:O 4:E:141:GLN:CG 1.98 1.09

1:A:530:GLN:HG2 1:A:757:VAL:HG12 1.16 1.085:B:140:A:H5’ 8:H:396:VAL:HG11 1.34 1.08

4:E:135:LYS:HE2 4:E:137:ARG:CD 1.83 1.071:A:529:PRO:CB 1:A:554:GLN:HG2 1.83 1.075:B:121:G:C1’ 8:H:517:LYS:HA 1.86 1.064:E:135:LYS:CE 4:E:137:ARG:HD3 1.86 1.054:E:58:TYR:HE2 4:E:136:MET:HG2 1.16 1.051:A:530:GLN:CG 1:A:757:VAL:HG12 1.76 1.047:G:47:UNK:O 7:G:77:UNK:O 1.76 1.04

1:A:626:ILE:HG12 1:A:770:GLY:HA2 1.33 1.035:B:121:G:C1’ 8:H:520:GLU:HB3 1.89 1.02

1:A:529:PRO:HA 1:A:554:GLN:HE21 1.23 1.021:A:530:GLN:HG2 1:A:757:VAL:HG13 1.03 1.001:A:824:GLN:O 1:A:828:LEU:HB2 1.62 1.005:B:121:G:OP1 8:H:518:LYS:CA 2.10 1.005:B:122:A:N7 8:H:518:LYS:CG 2.26 0.995:B:121:G:C1’ 8:H:517:LYS:CA 2.40 0.991:A:593:ILE:O 1:A:597:PHE:HB3 1.63 0.985:B:146:G:O2’ 8:H:528:LYS:HE3 1.63 0.981:A:912:LEU:O 1:A:916:LEU:HB2 1.63 0.987:G:51:UNK:CA 7:G:73:UNK:O 2.12 0.984:E:58:TYR:CE2 4:E:136:MET:HG2 2.01 0.95

5:B:121:G:P 8:H:518:LYS:CA 2.53 0.951:A:530:GLN:HG2 1:A:757:VAL:HG11 1.48 0.947:G:51:UNK:CB 7:G:73:UNK:C 2.44 0.947:G:97:UNK:O 7:G:123:UNK:CB 2.17 0.92

2:D:577:GLN:OE1 2:D:579:ILE:HB 1.69 0.911:A:626:ILE:HB 1:A:770:GLY:N 1.86 0.905:B:140:A:H5’ 8:H:396:VAL:HG12 1.52 0.89

1:A:529:PRO:HB2 1:A:554:GLN:HG2 1.53 0.891:A:626:ILE:HG13 1:A:771:ILE:HG12 1.54 0.881:A:626:ILE:CD1 1:A:771:ILE:HG12 2.04 0.885:B:121:G:OP1 8:H:518:LYS:CB 2.23 0.867:G:51:UNK:HA 7:G:73:UNK:C 2.06 0.86





Clashoverlap (Å)

5:B:122:A:C8 8:H:518:LYS:CG 2.58 0.861:A:530:GLN:CG 1:A:757:VAL:HG13 1.87 0.854:E:140:ALA:C 4:E:141:GLN:HG2 1.97 0.851:A:787:GLY:O 1:A:791:GLU:HB2 1.76 0.85

1:A:658:ARG:HH22 1:A:697:ASN:HB2 1.42 0.848:H:412:ASP:C 8:H:460:GLY:CA 2.40 0.831:A:462:PHE:O 1:A:466:LYS:HB2 1.79 0.821:A:1017:ILE:O 1:A:1021:PHE:HB2 1.81 0.811:A:626:ILE:CG1 1:A:771:ILE:HG12 2.10 0.811:A:984:THR:O 1:A:988:PHE:HB3 1.81 0.807:G:75:UNK:CB 7:G:110:UNK:C 2.58 0.801:A:529:PRO:CA 1:A:554:GLN:HG2 2.11 0.807:G:51:UNK:N 7:G:74:UNK:CB 2.45 0.805:B:122:A:H2 8:H:407:TYR:CG 2.00 0.795:B:117:U:C1’ 8:H:526:PHE:HB2 2.12 0.79

2:D:572:CYS:SG 2:D:579:ILE:HB 2.23 0.795:B:120:C:C4 8:H:522:ARG:HA 2.18 0.79

4:E:136:MET:HG3 4:E:142:ILE:HD11 1.65 0.797:G:75:UNK:CB 7:G:110:UNK:O 2.32 0.785:B:86:U:O2 5:B:88:C:N4 2.17 0.77

1:A:626:ILE:CG1 1:A:770:GLY:CA 2.60 0.771:A:582:LYS:HA 1:A:787:GLY:HA2 1.67 0.764:E:39:ILE:HD11 4:E:136:MET:CE 2.15 0.765:B:117:U:O4’ 8:H:526:PHE:HD2 1.69 0.76

4:E:39:ILE:HD11 4:E:136:MET:HE3 1.67 0.757:G:51:UNK:HA 7:G:74:UNK:CA 2.16 0.751:A:549:LEU:O 1:A:554:GLN:OE1 2.04 0.754:E:59:GLU:HA 4:E:63:ALA:HA 1.70 0.745:B:128:G:N2 5:B:142:C:O2 2.18 0.745:B:140:A:O2’ 8:H:393:ALA:HA 1.88 0.73

1:A:530:GLN:HG3 1:A:757:VAL:HG12 1.68 0.733:F:42:VAL:HG13 3:F:58:ASN:HD21 1.53 0.735:B:121:G:OP1 8:H:518:LYS:HG2 1.88 0.734:E:135:LYS:NZ 4:E:137:ARG:HD3 2.03 0.73

1:A:651:LEU:HD23 1:A:700:GLU:HB3 1.71 0.735:B:121:G:OP2 8:H:521:PHE:CB 2.34 0.73

1:A:766:ARG:HH22 1:A:772:PRO:HD3 1.54 0.721:A:529:PRO:CA 1:A:554:GLN:HE21 1.99 0.721:A:529:PRO:HA 1:A:554:GLN:NE2 2.01 0.721:A:617:LEU:HB3 1:A:817:TYR:HB3 1.73 0.711:A:889:LYS:HA 1:A:945:GLN:HE22 1.54 0.71





Clashoverlap (Å)

5:B:141:U:H4’ 8:H:392:LYS:HD3 1.73 0.703:F:33:CYS:H 3:F:44:GLU:HA 1.54 0.707:G:74:UNK:O 7:G:111:UNK:N 2.25 0.705:B:128:G:N1 5:B:142:C:N3 2.36 0.70

1:A:103:LYS:HG3 2:D:640:ARG:HH22 1.56 0.705:B:122:A:C8 8:H:518:LYS:CD 2.75 0.69

1:A:558:LYS:HA 1:A:561:LEU:HD12 1.75 0.695:B:94:A:H3’ 5:B:95:G:H21 1.57 0.69

2:D:572:CYS:SG 2:D:579:ILE:CG2 2.80 0.694:E:135:LYS:HE2 4:E:137:ARG:CG 2.23 0.694:E:46:ALA:CB 4:E:138:LYS:HE3 2.18 0.685:B:70:A:H2 5:B:88:C:H41 1.40 0.68

1:A:630:LYS:O 1:A:788:LYS:NZ 2.25 0.685:B:121:G:H2’ 8:H:517:LYS:HB3 1.76 0.688:H:412:ASP:O 8:H:460:GLY:HA3 1.93 0.681:A:626:ILE:CB 1:A:770:GLY:HA2 2.23 0.685:B:43:C:H4’ 5:B:44:A:H5’ 1.74 0.675:B:122:A:C2 8:H:407:TYR:CG 2.82 0.67

1:A:790:GLU:OE2 1:A:812:ARG:NH1 2.26 0.671:A:944:ARG:O 1:A:948:HIS:HB2 1.93 0.674:E:56:ASN:HA 4:E:138:LYS:HB2 1.76 0.675:B:140:A:C4’ 8:H:396:VAL:HG11 2.25 0.67

2:D:514:TYR:HA 2:D:536:TYR:HB3 1.77 0.673:F:14:LEU:HD21 3:F:47:PRO:HD2 1.77 0.671:A:528:TYR:HB3 1:A:530:GLN:NE2 2.09 0.661:A:643:ASP:H 1:A:740:ILE:HA 1.59 0.665:B:149:U:H2’ 5:B:150:G:H8 1.60 0.665:B:121:G:OP1 8:H:518:LYS:CG 2.42 0.66

2:D:612:ASN:HD22 2:D:620:VAL:HG13 1.59 0.661:A:615:VAL:HB 1:A:819:PHE:HB2 1.77 0.661:A:923:LEU:HA 1:A:927:GLN:HE21 1.61 0.667:G:75:UNK:CB 7:G:110:UNK:CB 2.73 0.661:A:1051:LEU:HA 1:A:1054:ILE:HD12 1.77 0.667:G:100:UNK:HA 7:G:121:UNK:CB 2.26 0.665:B:140:A:C5’ 8:H:396:VAL:CG1 2.52 0.65

2:D:564:LYS:HB3 6:C:6:DG:H4’ 1.78 0.654:E:140:ALA:O 4:E:141:GLN:CB 2.44 0.651:A:626:ILE:HB 1:A:770:GLY:CA 2.26 0.651:A:481:LYS:HB3 1:A:484:GLU:HB2 1.79 0.655:B:121:G:O4’ 8:H:521:PHE:N 2.29 0.655:B:122:A:N7 8:H:518:LYS:HG2 1.99 0.65





Clashoverlap (Å)

7:G:71:UNK:O 7:G:73:UNK:N 2.29 0.651:A:168:GLN:NE2 1:A:172:VAL:O 2.28 0.651:A:331:CYS:O 1:A:492:ARG:NH1 2.30 0.652:D:572:CYS:SG 2:D:577:GLN:O 2.52 0.648:H:464:ILE:N 8:H:464:ILE:HD12 2.12 0.641:A:127:SER:O 1:A:131:LEU:N 2.29 0.641:A:913:LYS:NZ 5:B:58:A:N7 2.41 0.644:E:88:LYS:HG2 4:E:97:GLU:HG2 1.79 0.647:G:49:UNK:O 7:G:75:UNK:O 2.15 0.641:A:139:LEU:O 1:A:143:PHE:HB2 1.97 0.64

2:D:577:GLN:OE1 2:D:579:ILE:CB 2.43 0.645:B:121:G:H2’ 8:H:517:LYS:HD2 1.79 0.64

3:F:100:ASP:OD1 3:F:104:LYS:NZ 2.32 0.632:D:631:ILE:HA 2:D:636:GLU:HB3 1.81 0.631:A:229:ILE:HD11 1:A:472:LEU:HB2 1.80 0.631:A:528:TYR:CB 1:A:530:GLN:NE2 2.62 0.631:A:538:LYS:HE2 1:A:543:ARG:HD3 1.79 0.631:A:1103:LEU:O 1:A:1107:ILE:N 2.30 0.634:E:118:ILE:HG23 4:E:126:ARG:HG2 1.79 0.633:F:104:LYS:O 3:F:108:LEU:HB2 1.98 0.63

1:A:1007:LEU:HD13 1:A:1009:PHE:HB2 1.80 0.631:A:113:THR:HB 1:A:120:GLU:H 1.63 0.634:E:68:ILE:HG12 4:E:133:MET:HG2 1.79 0.631:A:539:LYS:HG3 1:A:541:SER:H 1.62 0.631:A:626:ILE:HD11 1:A:771:ILE:HG12 1.81 0.632:D:553:TYR:HA 2:D:583:VAL:HA 1.80 0.637:G:84:UNK:HA 7:G:99:UNK:HA 1.81 0.625:B:126:U:H3 5:B:144:A:H2 1.45 0.62

7:G:51:UNK:CA 7:G:73:UNK:C 2.66 0.621:A:397:ASN:ND2 1:A:427:ASP:O 2.33 0.621:A:460:ILE:HA 1:A:463:ILE:HD12 1.82 0.621:A:594:SER:O 1:A:598:ALA:HB3 2.00 0.621:A:579:LEU:O 1:A:581:GLN:NE2 2.31 0.62

1:A:605:LYS:HG2 1:A:610:PRO:HA 1.81 0.621:A:412:LYS:NZ 1:A:899:ILE:O 2.32 0.621:A:975:TYR:O 1:A:979:TYR:HB2 2.00 0.621:A:945:GLN:O 1:A:949:HIS:ND1 2.25 0.62

1:A:1070:GLN:NE2 1:A:1074:SER:OG 2.33 0.621:A:224:ILE:O 1:A:416:ASN:ND2 2.33 0.61

1:A:314:ILE:HG23 1:A:387:CYS:HB3 1.82 0.611:A:589:ASP:OD1 1:A:590:ASN:ND2 2.33 0.61





Clashoverlap (Å)

5:B:107:G:H3’ 5:B:108:A:H8 1.65 0.611:A:702:GLN:NE2 1:A:703:ILE:O 2.30 0.611:A:1103:LEU:HA 1:A:1106:LYS:HB2 1.81 0.611:A:63:THR:HG23 1:A:159:THR:HG22 1.83 0.611:A:626:ILE:HG13 1:A:770:GLY:HA2 1.80 0.602:D:560:LYS:N 6:C:2:DT:OP1 2.33 0.60

1:A:1080:LEU:HA 1:A:1084:GLU:HB3 1.81 0.607:G:139:UNK:O 7:G:143:UNK:N 2.35 0.607:G:51:UNK:HA 7:G:74:UNK:N 2.15 0.602:D:652:ILE:HB 2:D:676:GLU:HB2 1.83 0.602:D:573:GLU:O 2:D:576:GLN:NE2 2.34 0.60

2:D:642:LEU:HD12 2:D:645:LYS:HD2 1.84 0.602:D:689:LYS:O 2:D:693:HIS:ND1 2.31 0.60

1:A:881:ILE:HG12 1:A:888:ILE:HG23 1.82 0.601:A:626:ILE:HB 1:A:770:GLY:H 1.64 0.603:F:78:LEU:HB2 3:F:82:ILE:HB 1.83 0.601:A:949:HIS:O 1:A:953:THR:OG1 2.20 0.595:B:120:C:N3 8:H:522:ARG:CB 2.65 0.597:G:51:UNK:C 7:G:74:UNK:CB 2.79 0.59

1:A:125:ASN:OD1 1:A:127:SER:OG 2.17 0.591:A:241:VAL:HG21 1:A:471:VAL:HG22 1.84 0.595:B:110:A:OP2 5:B:155:A:N6 2.35 0.59

1:A:539:LYS:HE3 1:A:541:SER:HB3 1.83 0.591:A:750:LYS:HG2 1:A:754:GLN:HE22 1.66 0.591:A:615:VAL:HG21 1:A:831:ILE:HD11 1.85 0.59

1:A:888:ILE:O 1:A:945:GLN:NE2 2.34 0.593:F:110:GLN:O 3:F:115:SER:OG 2.20 0.595:B:95:G:OP2 5:B:95:G:N2 2.35 0.595:B:140:A:H4’ 8:H:396:VAL:CG1 2.33 0.595:B:60:U:O2’ 5:B:61:G:N2 2.35 0.59

1:A:1008:GLN:HB3 1:A:1012:GLU:HB2 1.85 0.591:A:1098:GLN:NE2 1:A:1102:THR:OG1 2.35 0.59

1:A:463:ILE:O 1:A:467:ILE:HB 2.02 0.591:A:648:ASN:ND2 1:A:705:TYR:OH 2.36 0.591:A:157:VAL:HB 1:A:170:ALA:HB3 1.84 0.591:A:237:ARG:NE 5:B:36:U:O4 2.36 0.591:A:471:VAL:O 1:A:475:ASN:ND2 2.36 0.591:A:533:LEU:HA 1:A:546:MET:HG3 1.83 0.591:A:975:TYR:O 1:A:979:TYR:CB 2.51 0.59

1:A:161:VAL:HG22 1:A:167:LEU:HD11 1.85 0.591:A:239:PRO:HB2 1:A:323:PHE:HD2 1.68 0.59





Clashoverlap (Å)

1:A:738:ARG:HD2 7:G:3:UNK:HA 1.84 0.595:B:32:G:H2’ 5:B:33:A:C8 2.37 0.595:B:122:A:N3 8:H:407:TYR:CD2 2.71 0.585:B:146:G:H4’ 5:B:147:G:H4’ 1.86 0.58

3:F:74:ARG:NH2 4:E:129:TYR:OH 2.35 0.581:A:528:TYR:HB2 1:A:530:GLN:HE22 1.68 0.581:A:594:SER:HA 1:A:597:PHE:HD2 1.69 0.584:E:36:CYS:O 4:E:40:ASN:ND2 2.36 0.58

1:A:555:LYS:HA 1:A:558:LYS:HE2 1.84 0.581:A:812:ARG:HE 1:A:817:TYR:HB2 1.69 0.585:B:140:A:H4’ 8:H:396:VAL:HG11 1.85 0.585:B:47:C:H2’ 5:B:48:C:C6 2.39 0.585:B:117:U:O4’ 8:H:526:PHE:CD2 2.55 0.58

1:A:357:GLN:HE21 1:A:361:ASN:HD21 1.51 0.581:A:655:ARG:NH2 5:B:51:A:O3’ 2.36 0.584:E:67:ALA:HB3 4:E:134:LEU:HB2 1.86 0.587:G:78:UNK:N 7:G:105:UNK:O 2.36 0.58

1:A:583:ILE:HG13 1:A:790:GLU:HB3 1.85 0.581:A:984:THR:O 1:A:988:PHE:CB 2.51 0.583:F:14:LEU:HD11 3:F:47:PRO:HG2 1.86 0.587:G:89:UNK:O 7:G:94:UNK:N 2.36 0.582:D:572:CYS:SG 2:D:579:ILE:CB 2.90 0.584:E:114:GLN:OE1 4:E:147:PHE:N 2.37 0.574:E:43:VAL:HG12 4:E:47:LYS:HE3 1.85 0.575:B:117:U:C1’ 8:H:526:PHE:HD2 2.17 0.575:B:149:U:H2’ 5:B:150:G:C8 2.39 0.571:A:882:ASP:O 1:A:887:GLU:N 2.36 0.57

2:D:564:LYS:HD3 6:C:5:DG:H2” 1.85 0.571:A:981:LYS:HE3 1:A:983:ASN:HB2 1.86 0.571:A:971:LYS:NZ 5:B:137:U:OP2 2.33 0.572:D:563:LEU:N 2:D:571:PHE:O 2.38 0.571:A:110:ILE:O 1:A:734:GLN:NE2 2.37 0.57

1:A:796:PHE:HB2 1:A:797:LEU:HD22 1.86 0.571:A:849:LYS:H 1:A:869:SER:HB3 1.69 0.575:B:102:U:H2’ 5:B:103:G:H8 1.69 0.57

7:G:75:UNK:CB 7:G:110:UNK:CA 2.83 0.571:A:1030:TRP:HA 1:A:1033:ILE:HD12 1.86 0.571:A:156:LEU:HD11 1:A:172:VAL:HG12 1.87 0.571:A:390:ASN:O 1:A:394:GLY:N 2.38 0.566:C:9:DT:H2” 6:C:10:DG:H3’ 1.86 0.564:E:73:PHE:HA 4:E:89:LEU:HG 1.87 0.56





Clashoverlap (Å)

1:A:34:SER:OG 1:A:35:ASN:N 2.37 0.561:A:333:LEU:HD12 5:B:15:C:H2’ 1.86 0.563:F:18:MET:SD 3:F:22:ARG:NH2 2.79 0.561:A:787:GLY:O 1:A:791:GLU:CB 2.53 0.561:A:880:SER:O 1:A:889:LYS:N 2.33 0.563:F:78:LEU:N 3:F:82:ILE:O 2.36 0.561:A:394:GLY:O 1:A:398:PHE:N 2.35 0.565:B:117:U:C1’ 8:H:526:PHE:CB 2.83 0.56

1:A:794:THR:HG22 1:A:798:LYS:HE2 1.88 0.562:D:687:LEU:HD21 3:F:104:LYS:HD2 1.88 0.561:A:347:ILE:HA 1:A:351:GLU:HB3 1.86 0.56

1:A:110:ILE:HG22 1:A:734:GLN:HG3 1.87 0.561:A:881:ILE:HG23 1:A:888:ILE:HG12 1.88 0.555:B:111:A:H2’ 5:B:112:A:C8 2.41 0.555:B:52:A:O2’ 5:B:53:A:O4’ 2.24 0.55

2:D:661:GLU:HG2 2:D:663:ASN:H 1.71 0.557:G:53:UNK:CB 7:G:62:UNK:CB 2.84 0.551:A:576:LYS:HZ3 1:A:586:SER:HB3 1.71 0.552:D:537:VAL:HG23 2:D:653:PHE:HB2 1.87 0.551:A:156:LEU:HG 1:A:171:GLY:HA3 1.89 0.555:B:124:A:O2’ 5:B:148:A:O2’ 2.16 0.555:B:52:A:N6 6:C:13:DG:OP1 2.34 0.55

4:E:136:MET:HG3 4:E:142:ILE:CD1 2.35 0.553:F:57:ASP:OD1 3:F:60:ARG:NH2 2.39 0.551:A:303:GLU:HA 1:A:306:LEU:HD12 1.87 0.552:D:562:VAL:HA 2:D:572:CYS:HA 1.88 0.554:E:39:ILE:CG1 4:E:136:MET:HE1 2.36 0.551:A:129:GLN:NE2 7:G:107:UNK:O 2.40 0.555:B:140:A:O2’ 8:H:393:ALA:CA 2.54 0.55

1:A:944:ARG:NH2 1:A:1108:SER:O 2.39 0.555:B:121:G:C2’ 8:H:517:LYS:HB3 2.37 0.553:F:40:SER:O 3:F:60:ARG:NH2 2.35 0.551:A:233:ASN:H 1:A:234:HIS:CD2 2.25 0.541:A:786:PHE:O 1:A:790:GLU:HB2 2.07 0.545:B:102:U:H2’ 5:B:103:G:C8 2.42 0.54

1:A:1000:VAL:HA 1:A:1003:ILE:HG22 1.89 0.541:A:234:HIS:CD2 5:B:39:C:H2’ 2.42 0.541:A:229:ILE:HG23 1:A:478:ILE:HG21 1.88 0.547:G:99:UNK:O 7:G:121:UNK:O 2.24 0.54

1:A:626:ILE:HG13 1:A:770:GLY:C 2.27 0.545:B:47:C:H2’ 5:B:48:C:H6 1.70 0.54





Clashoverlap (Å)

1:A:849:LYS:HB3 1:A:850:ILE:HG23 1.90 0.543:F:40:SER:HB3 3:F:60:ARG:HE 1.72 0.545:B:115:A:N1 5:B:152:C:N4 2.56 0.54

2:D:553:TYR:OH 2:D:564:LYS:NZ 2.37 0.544:E:39:ILE:HG12 4:E:136:MET:HE1 1.90 0.541:A:694:TYR:HB2 1:A:696:PHE:HE1 1.73 0.544:E:39:ILE:HD11 4:E:136:MET:HE1 1.89 0.541:A:501:LYS:HA 1:A:504:ILE:HD12 1.89 0.541:A:961:MET:O 1:A:965:PHE:CB 2.55 0.54

1:A:533:LEU:HD23 1:A:760:PHE:HB2 1.90 0.541:A:96:SER:HA 1:A:99:LEU:HD12 1.90 0.544:E:135:LYS:HZ1 4:E:137:ARG:HD3 1.72 0.542:D:606:GLN:NE2 2:D:673:LEU:O 2.42 0.531:A:106:TYR:HB2 1:A:109:GLN:HG3 1.91 0.531:A:530:GLN:CB 1:A:757:VAL:HG13 2.37 0.531:A:723:GLN:NE2 1:A:724:SER:O 2.41 0.531:A:826:ASN:O 1:A:830:LEU:HB2 2.08 0.531:A:78:LYS:HZ3 4:E:104:LYS:HE3 1.74 0.531:A:360:GLU:O 1:A:364:ASN:ND2 2.42 0.531:A:649:LYS:HB3 1:A:731:VAL:HG12 1.91 0.532:D:543:SER:O 2:D:545:GLN:NE2 2.42 0.53

1:A:588:PHE:HE2 1:A:591:LYS:H 1.55 0.531:A:981:LYS:HG2 1:A:983:ASN:H 1.74 0.534:E:130:VAL:HG12 4:E:149:ILE:HA 1.90 0.532:D:660:LYS:NZ 6:C:4:DG:O6 2.42 0.532:D:524:ALA:HB1 2:D:668:ILE:HG21 1.89 0.534:E:100:ILE:HA 4:E:143:GLN:HE22 1.73 0.53

1:A:626:ILE:HG13 1:A:770:GLY:CA 2.36 0.535:B:112:A:H2’ 5:B:113:A:C8 2.43 0.53

1:A:384:ILE:HG21 1:A:401:PHE:HE2 1.72 0.532:D:656:GLN:HB2 2:D:673:LEU:HD11 1.90 0.531:A:626:ILE:HB 1:A:770:GLY:HA2 1.90 0.531:A:340:LEU:HA 1:A:343:GLN:HE21 1.73 0.521:A:626:ILE:CB 1:A:770:GLY:CA 2.86 0.521:A:336:ASN:N 1:A:336:ASN:OD1 2.43 0.521:A:536:ILE:HB 1:A:544:PRO:HA 1.89 0.521:A:827:ALA:HA 1:A:830:LEU:HD13 1.91 0.522:D:535:PHE:N 2:D:655:ILE:O 2.42 0.521:A:604:TRP:O 1:A:608:GLY:N 2.43 0.52

2:D:514:TYR:HE1 2:D:685:LYS:HB3 1.74 0.524:E:58:TYR:CE1 4:E:138:LYS:HD3 2.44 0.52





Clashoverlap (Å)

1:A:305:ASP:HA 1:A:308:LEU:HD12 1.92 0.521:A:626:ILE:HG13 1:A:771:ILE:N 2.24 0.525:B:121:G:O5’ 8:H:518:LYS:HA 2.09 0.522:D:586:MET:O 2:D:588:ARG:NH1 2.41 0.521:A:454:LYS:NZ 1:A:458:ASP:OD2 2.41 0.521:A:125:ASN:HB2 1:A:734:GLN:NE2 2.25 0.521:A:623:TYR:O 1:A:626:ILE:HG12 2.10 0.52

1:A:30:LEU:HD13 1:A:66:ALA:HB1 1.91 0.521:A:28:SER:HB3 1:A:693:PRO:HD2 1.91 0.521:A:790:GLU:O 1:A:794:THR:OG1 2.20 0.521:A:907:ILE:O 1:A:915:GLN:NE2 2.39 0.522:D:515:SER:N 2:D:536:TYR:O 2.40 0.522:D:572:CYS:N 2:D:577:GLN:O 2.33 0.527:G:97:UNK:C 7:G:123:UNK:CB 2.88 0.521:A:166:TYR:O 1:A:730:ILE:N 2.38 0.521:A:815:ASP:N 1:A:815:ASP:OD1 2.43 0.521:A:860:ASP:HA 1:A:863:LEU:HD12 1.90 0.523:F:27:THR:HA 3:F:74:ARG:HG2 1.91 0.525:B:140:A:H4’ 8:H:396:VAL:HB 1.92 0.52

1:A:528:TYR:CB 1:A:530:GLN:HE22 2.23 0.511:A:85:SER:OG 1:A:86:GLN:OE1 2.22 0.513:F:112:ASP:OD2 3:F:113:LYS:NZ 2.41 0.513:F:15:PHE:HA 3:F:21:PHE:HZ 1.75 0.517:G:53:UNK:O 7:G:61:UNK:N 2.43 0.51

1:A:479:THR:OG1 1:A:480:GLU:N 2.44 0.514:E:141:GLN:O 4:E:142:ILE:HD13 2.10 0.51

1:A:1034:VAL:HG22 1:A:1054:ILE:HD13 1.91 0.511:A:317:ASN:ND2 1:A:387:CYS:O 2.43 0.511:A:440:GLN:HA 1:A:443:THR:HB 1.91 0.511:A:741:THR:OG1 1:A:742:LYS:N 2.43 0.511:A:593:ILE:HD13 1:A:811:MET:HG3 1.93 0.514:E:107:ASP:HA 4:E:110:PRO:HD2 1.92 0.514:E:46:ALA:HB1 4:E:138:LYS:CE 2.22 0.511:A:599:GLN:NE2 1:A:934:PRO:O 2.42 0.514:E:125:ASN:O 4:E:128:LYS:NZ 2.44 0.514:E:58:TYR:CE2 4:E:136:MET:CG 2.84 0.514:E:91:ASP:OD1 4:E:94:GLY:N 2.44 0.513:F:55:VAL:HB 3:F:82:ILE:HA 1.91 0.514:E:58:TYR:HE2 4:E:136:MET:CG 2.05 0.511:A:81:GLN:HE22 4:E:82:SER:H 1.57 0.51

1:A:64:ILE:N 1:A:158:PHE:O 2.31 0.51Continued on next page...




Clashoverlap (Å)

1:A:642:GLN:HA 1:A:740:ILE:HG23 1.93 0.511:A:916:LEU:HG 1:A:992:ILE:HG12 1.93 0.511:A:916:LEU:HA 1:A:919:LYS:HB2 1.92 0.505:B:122:A:C2 8:H:407:TYR:CD2 2.98 0.50

1:A:534:ARG:HH11 1:A:545:ILE:HD11 1.76 0.501:A:882:ASP:OD1 1:A:884:ASN:ND2 2.44 0.506:C:17:DG:H2’ 6:C:18:DG:C8 2.46 0.503:F:112:ASP:O 3:F:116:SER:N 2.43 0.501:A:632:LEU:O 1:A:636:ASN:ND2 2.44 0.505:B:141:U:C5’ 8:H:392:LYS:HD3 2.41 0.50

1:A:507:LEU:HD21 1:A:765:PHE:HB2 1.93 0.501:A:1038:LYS:NZ 5:B:71:C:OP2 2.31 0.501:A:481:LYS:NZ 1:A:539:LYS:O 2.35 0.501:A:746:HIS:HA 1:A:749:LEU:HD12 1.93 0.501:A:905:VAL:HA 1:A:960:PHE:HE1 1.76 0.501:A:337:TYR:OH 5:B:16:A:O3’ 2.27 0.502:D:552:TYR:N 2:D:584:HIS:O 2.40 0.501:A:626:ILE:CD1 1:A:771:ILE:CG1 2.86 0.501:A:934:PRO:HB2 1:A:937:ASN:H 1.75 0.501:A:436:ASP:OD1 1:A:448:TYR:OH 2.29 0.501:A:594:SER:O 1:A:598:ALA:CB 2.60 0.50

1:A:924:PHE:CE1 5:B:51:A:H2’ 2.46 0.502:D:517:ILE:HD11 2:D:591:VAL:HG12 1.94 0.501:A:1017:ILE:O 1:A:1021:PHE:CB 2.55 0.501:A:624:ASP:HA 1:A:770:GLY:HA3 1.94 0.508:H:474:LEU:O 8:H:477:GLN:HG2 2.11 0.50

1:A:947:TYR:HB2 1:A:1032:ILE:HD11 1.94 0.491:A:608:GLY:O 1:A:609:ARG:NH1 2.38 0.492:D:533:LYS:HB3 2:D:657:PHE:CE1 2.47 0.491:A:749:LEU:HD23 1:A:752:ILE:HD11 1.93 0.491:A:123:ASN:HA 1:A:736:LYS:HE3 1.93 0.491:A:953:THR:O 1:A:957:PHE:HB2 2.13 0.491:A:53:ASP:O 1:A:57:GLN:N 2.46 0.491:A:614:TYR:O 1:A:851:THR:OG1 2.30 0.495:B:139:U:O2’ 8:H:400:ARG:NH1 2.46 0.491:A:235:MET:O 5:B:18:U:N3 2.46 0.491:A:412:LYS:N 1:A:415:GLU:OE1 2.45 0.495:B:120:C:C4 8:H:522:ARG:CA 2.94 0.49

1:A:658:ARG:NH2 1:A:697:ASN:HB2 2.20 0.492:D:518:GLU:HB2 2:D:595:THR:HB 1.94 0.492:D:564:LYS:NZ 6:C:6:DG:N3 2.61 0.49





Clashoverlap (Å)

1:A:1039:LYS:O 1:A:1041:LYS:NZ 2.44 0.481:A:27:ILE:HG21 1:A:695:TYR:HA 1.94 0.481:A:937:ASN:HB2 1:A:942:LEU:HD21 1.93 0.481:A:891:ILE:O 1:A:948:HIS:NE2 2.45 0.485:B:121:G:O4’ 8:H:520:GLU:HB3 2.11 0.481:A:14:LEU:HA 1:A:1002:LYS:HD2 1.96 0.481:A:452:LYS:HA 1:A:455:ILE:HD12 1.94 0.482:D:602:ILE:HG13 2:D:672:VAL:HG21 1.95 0.48

5:B:120:C:C5 8:H:522:ARG:HA 2.49 0.481:A:882:ASP:N 1:A:887:GLU:O 2.45 0.48

1:A:926:ASN:OD1 1:A:926:ASN:N 2.44 0.485:B:2:U:H4’ 5:B:3:A:H8 1.78 0.48

2:D:529:ILE:HG21 2:D:663:ASN:HD21 1.78 0.481:A:1053:LYS:NZ 5:B:61:G:N7 2.62 0.481:A:585:TYR:CD1 1:A:593:ILE:HG13 2.49 0.481:A:563:GLN:HG3 1:A:645:TYR:OH 2.13 0.481:A:701:ARG:CZ 1:A:703:ILE:HG12 2.44 0.481:A:619:ILE:HA 1:A:845:PHE:HB3 1.96 0.485:B:153:U:H2’ 5:B:154:U:C2 2.49 0.48

1:A:390:ASN:HB2 1:A:395:LYS:HA 1.95 0.481:A:400:VAL:O 1:A:404:LYS:HG2 2.13 0.48

1:A:446:ARG:HH21 5:B:134:C:H1’ 1.78 0.485:B:113:A:H2’ 5:B:114:G:C8 2.47 0.485:B:121:G:H2’ 8:H:517:LYS:CB 2.43 0.484:E:44:LYS:HA 4:E:47:LYS:HD2 1.96 0.485:B:61:G:O2’ 5:B:63:U:OP1 2.23 0.48

7:G:48:UNK:HA 7:G:77:UNK:O 2.13 0.484:E:65:GLU:OE2 4:E:137:ARG:HA 2.14 0.488:H:487:LEU:CB 8:H:498:VAL:HG22 2.43 0.481:A:492:ARG:HB2 1:A:495:ILE:HD12 1.94 0.481:A:652:LEU:HD11 1:A:727:ARG:HG3 1.96 0.481:A:742:LYS:HA 1:A:745:ILE:HD12 1.96 0.481:A:944:ARG:HA 1:A:947:TYR:CE1 2.49 0.485:B:117:U:C1’ 8:H:526:PHE:CD2 2.96 0.48

1:A:738:ARG:NH1 7:G:2:UNK:O 2.47 0.481:A:108:GLN:OE1 1:A:108:GLN:N 2.42 0.481:A:124:ILE:HG13 1:A:736:LYS:HG2 1.95 0.481:A:897:GLN:HA 1:A:900:ASN:HD22 1.78 0.486:C:9:DT:H1’ 6:C:10:DG:H8 1.78 0.48

2:D:560:LYS:HB3 2:D:573:GLU:HB2 1.96 0.481:A:1019:GLU:O 1:A:1023:ASN:ND2 2.47 0.47





Clashoverlap (Å)

1:A:1044:LYS:HA 1:A:1047:LEU:HB2 1.96 0.471:A:32:TYR:HB3 1:A:67:SER:HB3 1.96 0.471:A:532:LYS:HA 1:A:759:SER:H 1.79 0.475:B:122:A:N6 8:H:514:ILE:CB 2.77 0.475:B:146:G:N2 5:B:148:A:N7 2.60 0.47

2:D:608:SER:HA 2:D:611:ILE:HD12 1.95 0.471:A:694:TYR:HB2 1:A:696:PHE:CE1 2.49 0.478:H:515:LYS:HB3 8:H:515:LYS:NZ 2.29 0.471:A:298:PHE:HD2 1:A:304:ARG:HB2 1.80 0.471:A:529:PRO:C 1:A:554:GLN:NE2 2.68 0.47

1:A:614:TYR:HB2 1:A:818:LEU:HD11 1.96 0.471:A:529:PRO:C 1:A:554:GLN:HE21 2.17 0.471:A:910:LYS:HD2 5:B:135:U:H1’ 1.95 0.475:B:140:A:H4’ 8:H:396:VAL:CB 2.44 0.476:C:14:DT:H1’ 6:C:15:DT:C6 2.49 0.474:E:39:ILE:CD1 4:E:136:MET:HE1 2.45 0.472:D:651:PHE:HB2 2:D:653:PHE:CZ 2.50 0.472:D:606:GLN:HE22 2:D:674:LYS:HD2 1.79 0.474:E:70:THR:HG23 4:E:150:VAL:HG21 1.96 0.473:F:10:TYR:CG 3:F:74:ARG:HD3 2.48 0.477:G:51:UNK:HA 7:G:73:UNK:O 1.94 0.471:A:761:ASN:OD1 1:A:762:LYS:N 2.48 0.471:A:500:SER:O 1:A:503:THR:OG1 2.24 0.47

1:A:565:LEU:HD13 1:A:777:ILE:HB 1.96 0.471:A:961:MET:O 1:A:965:PHE:HB3 2.15 0.475:B:19:C:HO2’ 5:B:20:A:H8 1.63 0.472:D:554:ARG:N 2:D:582:GLN:O 2.33 0.47

1:A:123:ASN:HB2 1:A:734:GLN:HB3 1.96 0.471:A:124:ILE:H 1:A:734:GLN:HB3 1.79 0.471:A:314:ILE:HA 1:A:317:ASN:HD22 1.79 0.471:A:603:LYS:O 1:A:607:LYS:N 2.37 0.47

2:D:584:HIS:ND1 2:D:604:ASP:OD2 2.43 0.474:E:69:ILE:HA 4:E:159:HIS:CE1 2.50 0.473:F:19:ALA:O 3:F:24:LYS:NZ 2.39 0.47

1:A:1027:TRP:CD1 1:A:1058:ARG:HG2 2.49 0.471:A:418:LYS:N 1:A:421:ASP:OD2 2.41 0.47

1:A:612:LEU:HD23 1:A:822:ASP:HB3 1.97 0.471:A:997:VAL:HA 1:A:1000:VAL:HG12 1.96 0.461:A:1098:GLN:O 1:A:1102:THR:CB 2.63 0.46

1:A:1097:ILE:HD12 1:A:1100:ILE:HB 1.98 0.461:A:565:LEU:HD22 1:A:777:ILE:HA 1.96 0.46





Clashoverlap (Å)

1:A:954:VAL:O 1:A:957:PHE:N 2.45 0.461:A:958:TYR:HE1 1:A:1040:LYS:HG2 1.80 0.461:A:107:VAL:HG21 1:A:168:GLN:HG2 1.96 0.461:A:624:ASP:HB3 1:A:767:GLN:HE22 1.80 0.461:A:849:LYS:HB3 1:A:850:ILE:H 1.44 0.461:A:795:GLN:O 1:A:799:ASN:ND2 2.49 0.461:A:341:LYS:NZ 5:B:17:U:OP1 2.48 0.461:A:28:SER:OG 1:A:693:PRO:O 2.23 0.461:A:614:TYR:CG 1:A:874:CYS:HB2 2.51 0.463:F:35:GLU:O 3:F:37:GLN:NE2 2.48 0.465:B:71:C:H4’ 5:B:89:A:H61 1.80 0.46

1:A:404:LYS:HB3 1:A:422:TYR:CZ 2.51 0.465:B:46:C:HO2’ 5:B:47:C:C5’ 2.28 0.46

1:A:657:LYS:HD2 1:A:1002:LYS:HD2 1.97 0.462:D:646:LEU:HD23 2:D:646:LEU:HA 1.78 0.461:A:100:LEU:HD22 1:A:103:LYS:HD2 1.98 0.461:A:395:LYS:N 1:A:430:ASP:OD2 2.49 0.465:B:43:C:O4’ 6:C:7:DG:N2 2.37 0.46

2:D:591:VAL:HG23 2:D:600:VAL:HG21 1.97 0.461:A:380:LEU:HD21 1:A:405:LEU:HD22 1.98 0.451:A:53:ASP:OD2 1:A:56:PHE:N 2.37 0.452:D:598:ILE:HG22 2:D:600:VAL:HG13 1.97 0.454:E:136:MET:HA 4:E:142:ILE:HD12 1.97 0.451:A:241:VAL:HG22 1:A:475:ASN:HD21 1.82 0.451:A:594:SER:HA 1:A:597:PHE:CD2 2.50 0.451:A:232:CYS:HB3 1:A:493:LYS:HZ1 1.80 0.451:A:658:ARG:HH12 1:A:697:ASN:HD22 1.63 0.451:A:767:GLN:NE2 1:A:769:ARG:O 2.49 0.45

6:C:7:DG:H1’ 6:C:8:DT:C4 2.51 0.454:E:121:GLN:HE22 4:E:128:LYS:HG3 1.81 0.451:A:435:VAL:O 1:A:452:LYS:NZ 2.39 0.45

2:D:585:LEU:HD22 2:D:587:LEU:HD21 1.99 0.458:H:484:ASN:OD1 8:H:486:LYS:HG2 2.15 0.451:A:790:GLU:O 1:A:794:THR:CB 2.63 0.455:B:141:U:C4’ 8:H:392:LYS:HD3 2.45 0.45

1:A:1097:ILE:HD11 1:A:1101:LYS:HE3 1.98 0.451:A:849:LYS:HD3 1:A:849:LYS:HA 1.81 0.451:A:139:LEU:HA 1:A:139:LEU:HD23 1.84 0.451:A:19:ASP:O 1:A:22:THR:OG1 2.26 0.451:A:738:ARG:H 1:A:738:ARG:HD3 1.82 0.455:B:145:U:H5’ 5:B:146:G:H2’ 1.99 0.45





Clashoverlap (Å)

1:A:536:ILE:HD13 1:A:536:ILE:HA 1.77 0.451:A:551:LYS:HB2 1:A:554:GLN:HB2 1.97 0.451:A:658:ARG:HH12 1:A:697:ASN:ND2 2.15 0.452:D:566:HIS:HB3 5:B:42:U:C4 2.51 0.453:F:58:ASN:O 3:F:60:ARG:NH2 2.49 0.45

1:A:160:LYS:HD2 1:A:166:TYR:HE1 1.82 0.451:A:230:PHE:O 1:A:473:ARG:NH1 2.48 0.45

1:A:769:ARG:NH2 1:A:842:GLY:O 2.50 0.451:A:620:LYS:HG2 1:A:845:PHE:HA 1.98 0.451:A:911:ASN:OD1 1:A:911:ASN:N 2.50 0.451:A:961:MET:O 1:A:965:PHE:HB2 2.17 0.452:D:564:LYS:HZ1 6:C:6:DG:H21 1.65 0.451:A:239:PRO:HA 1:A:474:TYR:HE2 1.82 0.45

1:A:1004:LEU:HD21 1:A:1022:LYS:HB3 1.99 0.441:A:131:LEU:HA 1:A:136:PHE:CE2 2.52 0.441:A:529:PRO:HA 1:A:554:GLN:CG 2.47 0.441:A:583:ILE:HA 1:A:794:THR:HG21 1.98 0.441:A:927:GLN:OE1 1:A:953:THR:OG1 2.32 0.441:A:389:PRO:HB2 1:A:392:LEU:H 1.83 0.441:A:825:GLN:O 1:A:829:ASN:ND2 2.50 0.441:A:849:LYS:HB2 1:A:869:SER:H 1.82 0.444:E:146:TYR:HE2 4:E:148:SER:HB2 1.82 0.441:A:641:ILE:HG22 1:A:642:GLN:H 1.82 0.441:A:912:LEU:HB3 1:A:975:TYR:CE2 2.52 0.441:A:979:TYR:CE1 1:A:987:ASN:HB2 2.52 0.441:A:760:PHE:H 1:A:763:VAL:HG12 1.82 0.441:A:76:LYS:H 1:A:76:LYS:HG2 1.65 0.441:A:958:TYR:O 1:A:962:THR:OG1 2.22 0.44

2:D:588:ARG:NH2 6:C:3:DT:O2 2.51 0.444:E:170:ARG:HE 4:E:174:ILE:HD11 1.83 0.443:F:12:ARG:HG2 3:F:27:THR:HB 2.00 0.445:B:96:U:H2’ 5:B:97:G:C8 2.53 0.44

4:E:114:GLN:HB3 4:E:147:PHE:HB3 1.98 0.447:G:137:UNK:O 7:G:139:UNK:N 2.50 0.441:A:12:GLN:O 1:A:1002:LYS:NZ 2.36 0.44

1:A:337:TYR:CZ 1:A:341:LYS:HD2 2.53 0.441:A:628:GLN:NE2 1:A:768:LYS:O 2.49 0.444:E:63:ALA:H 4:E:170:ARG:NH2 2.16 0.44

1:A:797:LEU:HD11 1:A:833:GLN:NE2 2.32 0.445:B:46:C:O2’ 5:B:47:C:H6 2.01 0.44

1:A:1046:TYR:HD1 1:A:1049:LYS:HG3 1.82 0.44Continued on next page...




Clashoverlap (Å)

1:A:552:ASP:N 1:A:552:ASP:OD1 2.48 0.441:A:569:GLN:HE21 1:A:573:ARG:NH2 2.16 0.441:A:809:LEU:HA 1:A:810:LEU:HD12 2.00 0.442:D:568:ASP:HB3 2:D:571:PHE:HB2 1.99 0.442:D:682:GLU:HA 2:D:685:LYS:HG2 2.00 0.444:E:77:GLN:HB3 4:E:86:MET:HB3 2.00 0.444:E:79:ILE:HD11 4:E:86:MET:HB2 1.99 0.441:A:115:ILE:HG12 2:D:590:PHE:CE2 2.53 0.431:A:137:ARG:O 1:A:141:ASN:ND2 2.51 0.43

1:A:340:LEU:HD23 1:A:343:GLN:HE21 1.81 0.431:A:932:PHE:HZ 1:A:946:LEU:HB2 1.83 0.435:B:31:A:H5” 5:B:32:G:H8 1.83 0.43

4:E:102:LYS:HB2 4:E:107:ASP:H 1.83 0.434:E:117:GLU:HB2 4:E:147:PHE:HE2 1.83 0.431:A:20:LEU:HD22 1:A:166:TYR:HD2 1.84 0.431:A:525:PHE:CZ 1:A:751:HIS:HD2 2.37 0.43

1:A:985:ASN:HD22 1:A:989:LEU:HD12 1.82 0.434:E:130:VAL:HG12 4:E:149:ILE:HG13 2.00 0.43

3:F:40:SER:O 3:F:58:ASN:N 2.45 0.431:A:355:ASN:N 1:A:355:ASN:OD1 2.49 0.43

1:A:889:LYS:HD2 1:A:945:GLN:NE2 2.34 0.435:B:71:C:O2’ 5:B:90:A:N6 2.47 0.435:B:140:A:O2’ 8:H:393:ALA:CB 2.66 0.43

1:A:229:ILE:HD12 1:A:229:ILE:HA 1.75 0.431:A:642:GLN:O 1:A:708:TYR:HB3 2.18 0.435:B:125:U:H2’ 5:B:126:U:C6 2.53 0.431:A:567:ASP:N 1:A:567:ASP:OD1 2.49 0.43

1:A:613:TYR:CD2 1:A:824:GLN:HB2 2.53 0.431:A:622:CYS:HB2 1:A:786:PHE:HE2 1.83 0.435:B:124:A:H2’ 5:B:125:U:C6 2.54 0.435:B:44:A:HO2’ 5:B:45:A:H8 1.64 0.43

2:D:654:GLU:HG2 2:D:673:LEU:HD12 2.00 0.431:A:113:THR:O 1:A:119:VAL:HA 2.19 0.43

1:A:809:LEU:HD23 1:A:809:LEU:HA 1.73 0.434:E:60:TRP:HD1 4:E:167:TYR:CE1 2.36 0.431:A:696:PHE:HD2 1:A:699:LYS:HE2 1.84 0.431:A:894:GLN:HE22 1:A:896:GLN:HB3 1.84 0.432:D:593:ASP:OD1 2:D:596:GLY:N 2.34 0.431:A:1001:CYS:O 1:A:1022:LYS:HD2 2.19 0.43

1:A:393:LEU:HD12 1:A:398:PHE:HD1 1.84 0.431:A:440:GLN:OE1 1:A:444:GLN:N 2.51 0.43





Clashoverlap (Å)

1:A:797:LEU:HA 1:A:797:LEU:HD13 1.70 0.431:A:909:ILE:HG23 5:B:135:U:C5 2.54 0.431:A:979:TYR:OH 1:A:983:ASN:O 2.28 0.435:B:119:U:H2’ 5:B:120:C:O4’ 2.19 0.435:B:90:A:H2’ 5:B:91:A:C8 2.54 0.435:B:94:A:H3’ 5:B:95:G:N2 2.30 0.43

2:D:572:CYS:SG 2:D:579:ILE:HG21 2.56 0.431:A:1079:GLN:NE2 1:A:1081:ASN:OD1 2.40 0.431:A:481:LYS:HA 1:A:481:LYS:HD3 1.78 0.431:A:637:GLN:NE2 1:A:639:ASP:OD2 2.52 0.431:A:797:LEU:HD12 1:A:830:LEU:HG 2.00 0.431:A:873:GLU:HG3 1:A:882:ASP:HA 2.01 0.432:D:554:ARG:HD3 2:D:559:GLY:HA2 2.00 0.431:A:316:GLN:O 1:A:320:ASN:ND2 2.52 0.421:A:396:LYS:N 1:A:430:ASP:OD2 2.38 0.421:A:392:LEU:HA 1:A:433:TRP:HE1 1.83 0.421:A:912:LEU:HB3 1:A:975:TYR:HE2 1.83 0.42

5:B:22:A:H2’ 5:B:23:U:C6 2.53 0.425:B:37:G:H2’ 5:B:38:U:C6 2.54 0.42

1:A:993:LEU:HD11 1:A:1033:ILE:HD13 2.00 0.423:F:33:CYS:HB3 3:F:43:ILE:HG22 2.01 0.421:A:105:ASN:HB3 1:A:173:CYS:SG 2.59 0.421:A:565:LEU:O 1:A:565:LEU:HG 2.18 0.42

1:A:565:LEU:HD21 1:A:780:VAL:HB 2.01 0.421:A:882:ASP:HB3 1:A:887:GLU:HB3 2.01 0.421:A:622:CYS:SG 1:A:623:TYR:N 2.92 0.422:D:534:GLU:OE2 2:D:656:GLN:NE2 2.52 0.424:E:74:GLU:HA 4:E:127:HIS:CD2 2.55 0.42

1:A:1017:ILE:HD12 1:A:1020:ILE:HB 2.02 0.421:A:623:TYR:HD2 1:A:773:GLN:HG2 1.84 0.426:C:16:DG:H2’ 6:C:17:DG:C8 2.55 0.42

2:D:682:GLU:HG2 2:D:682:GLU:H 1.53 0.424:E:134:LEU:HD22 4:E:142:ILE:HG22 2.00 0.423:F:114:LEU:O 3:F:118:PHE:N 2.43 0.423:F:79:ASN:N 3:F:79:ASN:OD1 2.51 0.421:A:103:LYS:O 1:A:104:GLN:NE2 2.53 0.421:A:175:ASN:O 1:A:178:PHE:N 2.47 0.421:A:406:TYR:O 1:A:410:GLN:HB2 2.19 0.42

1:A:593:ILE:HG21 1:A:593:ILE:HD13 1.85 0.421:A:21:LEU:HD21 1:A:64:ILE:HD12 2.02 0.421:A:920:LEU:HA 1:A:920:LEU:HD13 1.70 0.42





Clashoverlap (Å)

5:B:101:A:H2’ 5:B:102:U:H6 1.85 0.424:E:127:HIS:H 4:E:128:LYS:HZ3 1.65 0.421:A:396:LYS:NZ 1:A:430:ASP:OD1 2.36 0.421:A:29:ALA:N 1:A:695:TYR:HE2 2.18 0.42

1:A:939:PHE:HA 1:A:942:LEU:HD12 2.02 0.428:H:487:LEU:HB3 8:H:498:VAL:HG22 2.02 0.425:B:138:U:O2’ 5:B:139:U:O4’ 2.37 0.42

4:E:29:GLN:HE22 4:E:65:GLU:HB3 1.85 0.421:A:1068:SER:HA 1:A:1071:LEU:HD12 2.00 0.421:A:131:LEU:HA 1:A:136:PHE:HE2 1.85 0.421:A:216:GLU:HB3 1:A:219:TYR:HD1 1.84 0.421:A:232:CYS:SG 1:A:233:ASN:N 2.93 0.421:A:548:PHE:HE2 1:A:775:LEU:HA 1.85 0.421:A:912:LEU:N 1:A:975:TYR:OH 2.47 0.42

1:A:328:LYS:HG2 5:B:15:C:N1 2.35 0.425:B:66:U:O2’ 5:B:68:U:OP2 2.37 0.42

4:E:108:GLU:O 4:E:111:GLU:HB3 2.20 0.423:F:21:PHE:HB2 3:F:22:ARG:HG3 2.01 0.421:A:380:LEU:HA 1:A:383:ILE:HD12 2.01 0.421:A:645:TYR:CD2 1:A:737:PRO:HB2 2.55 0.421:A:822:ASP:OD1 1:A:823:SER:N 2.53 0.421:A:979:TYR:CE2 1:A:981:LYS:HB3 2.55 0.422:D:625:GLN:O 2:D:629:ASN:ND2 2.52 0.42

1:A:1003:ILE:HD12 1:A:1003:ILE:HA 1.92 0.411:A:128:ARG:HA 1:A:131:LEU:HB2 2.01 0.411:A:534:ARG:NH1 1:A:545:ILE:HD11 2.35 0.411:A:622:CYS:HB3 1:A:815:ASP:HB3 2.02 0.411:A:424:CYS:HB3 5:B:136:A:C8 2.55 0.411:A:570:LEU:HD23 1:A:570:LEU:HA 1.81 0.411:A:638:SER:HA 1:A:742:LYS:HE3 2.01 0.411:A:727:ARG:HA 1:A:728:PRO:HD2 1.83 0.411:A:909:ILE:N 1:A:911:ASN:OD1 2.53 0.41

1:A:969:LEU:HD22 1:A:971:LYS:HE2 2.02 0.411:A:989:LEU:HA 1:A:992:ILE:HG22 2.02 0.411:A:995:TYR:O 1:A:998:GLU:HB3 2.20 0.415:B:86:U:H1’ 5:B:90:A:N1 2.34 0.41

2:D:514:TYR:CE1 2:D:685:LYS:HB3 2.54 0.414:E:138:LYS:HA 4:E:138:LYS:HD2 1.81 0.41

4:E:168:LEU:HD13 4:E:168:LEU:HA 1.86 0.411:A:95:ASP:O 1:A:99:LEU:N 2.46 0.41

1:A:1063:LYS:NZ 5:B:65:A:H5’ 2.35 0.41Continued on next page...




Clashoverlap (Å)

1:A:165:GLY:N 1:A:728:PRO:HB3 2.34 0.411:A:310:PHE:HD2 1:A:392:LEU:HD13 1.85 0.411:A:528:TYR:O 1:A:530:GLN:OE1 2.39 0.41

1:A:588:PHE:CE2 1:A:593:ILE:HG22 2.56 0.411:A:916:LEU:HD12 1:A:916:LEU:HA 1.92 0.41

5:B:151:U:H2’ 5:B:152:C:C6 2.54 0.418:H:486:LYS:HE2 8:H:497:ASP:OD2 2.19 0.411:A:389:PRO:HD2 1:A:392:LEU:HD23 2.02 0.411:A:59:PHE:CE2 1:A:135:ASN:HB3 2.56 0.411:A:1037:LEU:HB3 1:A:1047:LEU:HD22 2.02 0.411:A:224:ILE:HB 1:A:416:ASN:HD21 1.86 0.41

1:A:326:LEU:HD13 1:A:329:LYS:HD2 2.02 0.411:A:497:LYS:HE2 1:A:497:LYS:HB3 1.88 0.411:A:547:THR:HG22 5:B:46:C:H5’ 2.02 0.411:A:530:GLN:N 1:A:554:GLN:NE2 2.68 0.411:A:582:LYS:HG2 1:A:790:GLU:OE1 2.21 0.415:B:111:A:N1 5:B:154:U:H2’ 2.36 0.41

1:A:226:ARG:HD3 1:A:415:GLU:O 2.21 0.415:B:67:A:O2’ 5:B:68:U:O4’ 2.36 0.41

2:D:544:ILE:HG13 2:D:544:ILE:H 1.69 0.412:D:556:THR:OG1 2:D:584:HIS:NE2 2.52 0.414:E:84:LYS:HA 4:E:84:LYS:HD3 1.80 0.41

1:A:125:ASN:HB2 1:A:734:GLN:HE21 1.86 0.411:A:59:PHE:HE2 1:A:139:LEU:HD11 1.86 0.411:A:492:ARG:HA 1:A:492:ARG:HD2 1.92 0.416:C:15:DT:H2’ 6:C:16:DG:C8 2.56 0.414:E:166:ARG:O 4:E:170:ARG:HB2 2.21 0.413:F:105:LEU:O 3:F:109:SER:OG 2.28 0.418:H:464:ILE:N 8:H:464:ILE:CD1 2.81 0.41

1:A:1002:LYS:HD3 1:A:1002:LYS:HA 1.88 0.415:B:93:A:H2’ 5:B:94:A:H8 1.86 0.41

3:F:20:GLN:HA 3:F:24:LYS:HD2 2.03 0.411:A:1010:GLU:HB3 1:A:1086:GLU:HG3 2.01 0.411:A:20:LEU:HD22 1:A:166:TYR:CD2 2.56 0.411:A:330:PHE:HD2 1:A:379:PHE:HD1 1.67 0.411:A:364:ASN:OD1 1:A:540:GLY:HA3 2.21 0.41

5:B:6:C:H2’ 5:B:7:G:H8 1.86 0.412:D:563:LEU:HB2 2:D:573:GLU:HG2 2.02 0.414:E:61:TYR:CD2 4:E:171:LYS:HB2 2.56 0.411:A:1098:GLN:O 1:A:1102:THR:OG1 2.32 0.411:A:106:TYR:H 1:A:109:GLN:CD 2.24 0.41





Clashoverlap (Å)

1:A:133:SER:OG 1:A:136:PHE:N 2.45 0.411:A:106:TYR:CD1 1:A:172:VAL:HA 2.56 0.412:D:566:HIS:HB2 5:B:41:U:C5 2.56 0.414:E:84:LYS:HG3 4:E:102:LYS:HG2 2.02 0.411:A:572:PHE:O 1:A:576:LYS:HB3 2.22 0.401:A:921:ARG:C 1:A:923:LEU:H 2.24 0.40

1:A:446:ARG:HG3 5:B:137:U:C4 2.56 0.404:E:100:ILE:HG22 4:E:144:LEU:HB3 2.03 0.403:F:69:LYS:HB2 3:F:69:LYS:HE2 1.90 0.407:G:71:UNK:C 7:G:73:UNK:N 2.84 0.405:B:140:A:C4’ 8:H:396:VAL:CG1 2.93 0.40

8:H:487:LEU:HB2 8:H:498:VAL:HG22 2.02 0.401:A:1093:LEU:C 1:A:1098:GLN:HE21 2.24 0.401:A:361:ASN:HA 1:A:364:ASN:HD22 1.86 0.401:A:419:VAL:HG12 1:A:423:ILE:HD11 2.04 0.401:A:987:ASN:HA 1:A:990:LYS:HB3 2.03 0.40

2:D:627:VAL:HG13 2:D:639:ILE:HG21 2.04 0.403:F:51:ASN:HA 3:F:53:HIS:CD2 2.56 0.403:F:71:VAL:HG22 3:F:90:GLU:HG2 2.03 0.408:H:382:LYS:O 8:H:498:VAL:HA 2.20 0.401:A:1068:SER:O 1:A:1072:ILE:HG12 2.21 0.401:A:440:GLN:HB3 1:A:448:TYR:HD1 1.87 0.401:A:646:PHE:HE2 1:A:707:LEU:HB3 1.86 0.401:A:646:PHE:CZ 1:A:707:LEU:HD23 2.56 0.405:B:121:G:OP1 8:H:518:LYS:HB3 2.14 0.40

2:D:554:ARG:HB3 2:D:584:HIS:CD2 2.56 0.402:D:563:LEU:HG 2:D:565:TYR:HB2 2.04 0.402:D:572:CYS:SG 2:D:579:ILE:HG22 2.59 0.401:A:536:ILE:H 1:A:544:PRO:HA 1.87 0.40

1:A:886:LEU:HA 1:A:886:LEU:HD12 1.89 0.401:A:934:PRO:HB3 1:A:937:ASN:ND2 2.36 0.401:A:996:THR:HA 1:A:999:ASP:OD2 2.22 0.405:B:140:A:H2’ 5:B:141:U:C6 2.57 0.40

2:D:516:SER:HB2 2:D:595:THR:HG21 2.04 0.404:E:65:GLU:CD 4:E:136:MET:O 2.51 0.403:F:10:TYR:CE1 3:F:25:LYS:HB3 2.57 0.405:B:21:G:O2’ 5:B:22:A:O4’ 2.40 0.40

2:D:591:VAL:O 2:D:598:ILE:N 2.42 0.402:D:661:GLU:HG2 2:D:663:ASN:N 2.34 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 970/1117 (87%) 784 (81%) 178 (18%) 8 (1%) 19 59

2 D 183/701 (26%) 162 (88%) 19 (10%) 2 (1%) 14 51

3 F 111/121 (92%) 93 (84%) 18 (16%) 0 100 100

4 E 147/269 (55%) 122 (83%) 24 (16%) 1 (1%) 22 62

8 H 104/542 (19%) 104 (100%) 0 0 100 100

All All 1515/2750 (55%) 1265 (84%) 239 (16%) 11 (1%) 26 62

All (11) Ramachandran outliers are listed below:

Mol Chain Res Type1 A 530 GLN1 A 123 ASN4 E 141 GLN2 D 661 GLU2 D 662 PHE1 A 17 LYS1 A 18 GLU1 A 1006 TYR1 A 85 SER1 A 116 GLY1 A 239 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.

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

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

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


Mol Chain Analysed Rotameric Outliers Percentiles

1 A 931/1069 (87%) 920 (99%) 11 (1%) 71 84

2 D 172/657 (26%) 171 (99%) 1 (1%) 86 92

3 F 107/114 (94%) 105 (98%) 2 (2%) 57 75

4 E 132/242 (54%) 132 (100%) 0 100 100

8 H 95/517 (18%) 94 (99%) 1 (1%) 73 85

All All 1437/2599 (55%) 1422 (99%) 15 (1%) 77 86

All (15) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type1 A 143 PHE1 A 352 ASN1 A 534 ARG1 A 631 LEU1 A 634 PHE1 A 738 ARG1 A 851 THR1 A 933 ASN1 A 960 PHE1 A 985 ASN1 A 1004 LEU2 D 640 ARG3 F 61 ARG3 F 100 ASP8 H 498 VAL

Sometimes sidechains can be flipped to improve hydrogen bonding and reduce clashes. All (44)such sidechains are listed below:

Mol Chain Res Type1 A 102 ASN1 A 141 ASN1 A 234 HIS1 A 248 ASN1 A 317 ASN1 A 319 HIS1 A 320 ASN1 A 343 GLN1 A 352 ASN1 A 357 GLN1 A 361 ASN



Continued from previous page...Mol Chain Res Type1 A 364 ASN1 A 475 ASN1 A 526 GLN1 A 554 GLN1 A 636 ASN1 A 648 ASN1 A 697 ASN1 A 748 HIS1 A 751 HIS1 A 754 GLN1 A 767 GLN1 A 804 ASN1 A 839 ASN1 A 841 ASN1 A 884 ASN1 A 896 GLN1 A 900 ASN1 A 927 GLN1 A 945 GLN1 A 985 ASN1 A 1016 ASN1 A 1023 ASN1 A 1070 GLN1 A 1098 GLN2 D 576 GLN2 D 606 GLN2 D 612 ASN2 D 629 ASN2 D 656 GLN3 F 52 GLN4 E 40 ASN4 E 127 HIS4 E 143 GLN

5.3.3 RNA i○

Mol Chain Analysed Backbone Outliers Pucker Outliers5 B 158/159 (99%) 103 (65%) 14 (8%)

All (103) RNA backbone outliers are listed below:

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


Mol Chain Res Type5 B 2 U5 B 3 A5 B 4 C5 B 8 C5 B 9 U5 B 11 A5 B 12 A5 B 13 U5 B 14 U5 B 16 A5 B 19 C5 B 20 A5 B 21 G5 B 22 A5 B 24 C5 B 25 U5 B 26 G5 B 27 U5 B 29 A5 B 30 U5 B 31 A5 B 32 G5 B 33 A5 B 34 A5 B 35 C5 B 36 U5 B 37 G5 B 38 U5 B 39 C5 B 40 A5 B 41 U5 B 42 U5 B 43 C5 B 44 A5 B 45 A5 B 46 C5 B 47 C5 B 49 C5 B 50 A5 B 51 A5 B 53 A5 B 54 A5 B 55 U



Continued from previous page...Mol Chain Res Type5 B 56 C5 B 57 U5 B 58 A5 B 59 G5 B 60 U5 B 61 G5 B 62 C5 B 63 U5 B 64 G5 B 66 U5 B 67 A5 B 68 U5 B 69 A5 B 71 C5 B 75 C5 B 76 A5 B 86 U5 B 88 C5 B 89 A5 B 90 A5 B 91 A5 B 92 U5 B 96 U5 B 101 A5 B 106 G5 B 108 A5 B 110 A5 B 111 A5 B 115 A5 B 116 C5 B 117 U5 B 118 A5 B 119 U5 B 122 A5 B 123 C5 B 124 A5 B 125 U5 B 126 U5 B 128 G5 B 129 A5 B 130 U5 B 131 A



Continued from previous page...Mol Chain Res Type5 B 132 C5 B 133 A5 B 134 C5 B 135 U5 B 136 A5 B 137 U5 B 138 U5 B 140 A5 B 143 A5 B 144 A5 B 145 U5 B 146 G5 B 147 G5 B 154 U5 B 155 A5 B 156 U5 B 157 U5 B 159 U

All (14) RNA pucker outliers are listed below:

Mol Chain Res Type5 B 3 A5 B 33 A5 B 34 A5 B 39 C5 B 41 U5 B 42 U5 B 43 C5 B 46 C5 B 53 A5 B 60 U5 B 65 A5 B 122 A5 B 136 A5 B 137 U

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#nonstandard_residues_and_ligands


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.

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-7821. 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: 128 Y Index: 128 Z Index: 128

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

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

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


The images above show central slices of the map in three orthogonal directions.

6.3 Largest variance slices i○

6.3.1 Primary map

X Index: 123 Y Index: 121 Z Index: 140

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

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

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


6.5 Mask visualisation i○

This section 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_7821_msk_1.map i○

X Y Z

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

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


7 Map analysis i○

This section contains the results of statistical analysis of the map.

7.1 Map-value distribution i○

The map-value distribution is plotted in 128 intervals along the x-axis. The y-axis is logarithmic.A spike in this graph at zero usually indicates that the volume has been masked.

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

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


7.2 Volume estimate i○

The volume at the recommended contour level is 121 nm3; this corresponds to an approximatemass of 109 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 0.208 Å−1

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


8 Fourier-Shell correlation i○

This section was not generated. No FSC curve or half-maps provided.

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


9 Map-model fit i○

This section contains information regarding the fit between EMDB map EMD-7821 and PDBmodel 6D6V. Per-residue inclusion information can be found in section 3 on page 6.

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 0.055at 50% transparency in yellow overlaid with a ribbon representation of the model coloured in blue.These images allow for the visual assessment of the quality of fit between the atomic model andthe map.

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

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


9.2 Atom inclusion i○

At the recommended contour level, 78% of all backbone atoms, 58% of all non-hydrogen atoms,are inside the map.

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

full wwpdb em validation report i - rcsbfull wwpdb em validation report i dec13,2020–05:16pmest...

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