Full wwPDB EM Validation Report O i - RCSB...Ideal geometry (DNA, RNA) : Parkinson et al. (1996) alidationV Pipeline (wwPDB-VP) : 2.15.1 Page 2 ullF wwPDB EM alidationV Report EMD-4272,

Full wwPDB EM Validation Report iO

Dec 6, 2020 � 04:03 AM GMT

PDB ID : 6FKIEMDB ID : EMD-4272

Title : Chloroplast F1Fo conformation 3Authors : Hahn, A.; Vonck, J.; Mills, D.J.; Meier, T.; Kuehlbrandt, W.

Deposited on : 2018-01-24Resolution : 4.30 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 speci�c help available everywhere you see the iO symbol.

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

EMDB validation analysis : 0.0.0.dev61Mogul : 1.8.5 (274361), CSD as541be (2020)

MolProbity : 4.02b-467buster-report : 1.1.7 (2018)

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

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

https://www.wwpdb.org/validation/2017/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-4272, 6FKI

1 Overall quality at a glance iO

The following experimental techniques were used to determine the structure:ELECTRON MICROSCOPY

The reported resolution of this entry is 4.30 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.

MetricWhole archive(#Entries)

EM structures(#Entries)

Ramachandran outliers 154571 4023Sidechain outliers 154315 3826

The table below summarises the geometric issues observed across the polymeric chains and their �tto 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

7 J 81

7 K 81

7 L 81

7 M 81

7 N 81

7 O 81

7 P 81

7 Q 81

7 R 81

7 S 81

7 T 81

8 A 507

8 C 507

8 E 507

9 B 498

9 D 498

9 F 498


2 Entry composition iO

There are 12 unique types of molecules in this entry. The entry contains 39231 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 ATP synthase subunit a, chloroplastic.

Mol Chain Residues Atoms AltConf Trace

1 a 223Total C N O S1741 1172 268 299 2

0 0

Molecule 2 is a protein called ATP synthase subunit b, chloroplastic.


2 b 161Total C N O S1299 812 236 246 5

0 0

Molecule 3 is a protein called ATP synthase delta chain, chloroplastic.


3 d 179Total C N O S1383 876 229 277 1

0 0

Molecule 4 is a protein called ATP synthase subunit b', chloroplastic.


4 p 143Total C N O S1124 713 182 224 5

0 0

Molecule 5 is a protein called ATP synthase epsilon chain, chloroplastic.


5 e 131Total C N O S1010 622 190 195 3

0 0

Molecule 6 is a protein called ATP synthase gamma chain, chloroplastic.


6 g 321Total C N O S2497 1574 429 482 12

0 0

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


Molecule 7 is a protein called ATP synthase subunit c, chloroplastic.


7 S 79Total C N O S544 355 90 98 1

0 0

7 N 79Total C N O S544 355 90 98 1

0 0

7 O 79Total C N O S544 355 90 98 1

0 0

7 P 79Total C N O S544 355 90 98 1

0 0

7 Q 79Total C N O S544 355 90 98 1

0 0

7 R 79Total C N O S544 355 90 98 1

0 0

7 M 79Total C N O S544 355 90 98 1

0 0

7 T 79Total C N O S544 355 90 98 1

0 0

7 G 79Total C N O S544 355 90 98 1

0 0

7 H 79Total C N O S544 355 90 98 1

0 0

7 L 79Total C N O S544 355 90 98 1

0 0

7 K 79Total C N O S544 355 90 98 1

0 0

7 J 79Total C N O S544 355 90 98 1

0 0

7 I 79Total C N O S544 355 90 98 1

0 0

Molecule 8 is a protein called ATP synthase subunit alpha, chloroplastic.


8 E 498Total C N O S3827 2408 661 745 13

0 0

8 A 501Total C N O S3849 2422 666 748 13

0 0

8 C 501Total C N O S3851 2423 667 748 13

0 0

Molecule 9 is a protein called ATP synthase subunit beta, chloroplastic.



9 F 479Total C N O S3627 2288 623 700 16

0 0

9 B 478Total C N O S3619 2282 622 699 16

0 0

9 D 480Total C N O S3636 2294 625 701 16

0 0

Molecule 10 is ADENOSINE-5'-TRIPHOSPHATE (three-letter code: ATP) (formula:C10H16N5O13P3).

Mol Chain Residues Atoms AltConf

10 E 1Total C N O P31 10 5 13 3

0

10 A 1Total C N O P31 10 5 13 3

0

10 C 1Total C N O P31 10 5 13 3

0

Molecule 11 is MAGNESIUM ION (three-letter code: MG) (formula: Mg).


11 B 1Total Mg1 1

0

11 A 1Total Mg1 1

0

11 D 1Total Mg1 1

0

Continued on next page...




11 C 1Total Mg1 1

0

11 E 1Total Mg1 1

0

Molecule 12 is ADENOSINE-5'-DIPHOSPHATE (three-letter code: ADP) (formula:C10H15N5O10P2).


12 B 1Total C N O P27 10 5 10 2

0

12 D 1Total C N O P27 10 5 10 2

0


3 Residue-property plots iO

These plots are drawn for all protein, RNA, DNA and oligosaccharide chains in the entry. The�rst 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 �t 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: ATP synthase subunit a, chloroplastic

Chain a:

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• Molecule 2: ATP synthase subunit b, chloroplastic

Chain b:

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• Molecule 3: ATP synthase delta chain, chloroplastic

Chain d:

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


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• Molecule 4: ATP synthase subunit b', chloroplastic

Chain p:

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• Molecule 5: ATP synthase epsilon chain, chloroplastic

Chain e:

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• Molecule 6: ATP synthase gamma chain, chloroplastic

Chain g:

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• Molecule 7: ATP synthase subunit c, chloroplastic

Chain S:

MET

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Chain N:

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Chain O:

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Chain Q:

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Chain R:

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Chain M:

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• Molecule 8: ATP synthase subunit alpha, chloroplastic

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4 Experimental information iO

Property Value SourceEM reconstruction method SINGLE PARTICLE DepositorImposed symmetry POINT, C1 DepositorNumber of particles used 14409 DepositorResolution determination method FSC 0.143 CUT-OFF DepositorCTF correction method PHASE FLIPPING ONLY DepositorMicroscope FEI TITAN KRIOS DepositorVoltage (kV) 300 DepositorElectron dose (e−/Å

2) 25 Depositor

Minimum defocus (nm) 1500 DepositorMaximum defocus (nm) 2500 DepositorMagni�cation 132953 DepositorImage detector FEI FALCON III (4k x 4k) DepositorMaximum map value 0.225 DepositorMinimum map value -0.142 DepositorAverage map value 0.000 DepositorMap value standard deviation 0.013 DepositorRecommended contour level 0.05 DepositorMap size (Å) 368.55, 368.55, 368.55 wwPDBMap dimensions 350, 350, 350 wwPDBMap angles (◦) 90.0, 90.0, 90.0 wwPDBPixel spacing (Å) 1.053, 1.053, 1.053 Depositor

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


5 Model quality iO

5.1 Standard geometry iO

Bond lengths and bond angles in the following residue types are not validated in this section: MG,ATP, ADP

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 ChainBond lengths Bond angles

RMSZ #|Z| >5 RMSZ #|Z| >51 a 0.47 0/1792 0.71 2/2454 (0.1%)2 b 0.32 0/1309 0.55 1/1754 (0.1%)3 d 0.43 0/1399 0.59 0/18984 p 0.41 1/1134 (0.1%) 0.63 2/1519 (0.1%)5 e 0.43 0/1019 0.65 0/13816 g 0.56 1/2526 (0.0%) 0.69 4/3412 (0.1%)7 G 0.36 0/551 0.59 0/7507 H 0.36 0/551 0.59 0/7507 I 0.36 0/551 0.59 0/7507 J 0.36 0/551 0.59 0/7507 K 0.36 0/551 0.59 0/7507 L 0.36 0/551 0.59 0/7507 M 0.36 0/551 0.59 0/7507 N 0.36 0/551 0.59 0/7507 O 0.36 0/551 0.59 0/7507 P 0.36 0/551 0.59 0/7507 Q 0.36 0/551 0.59 0/7507 R 0.36 0/551 0.59 0/7507 S 0.36 0/551 0.59 0/7507 T 0.36 0/551 0.59 0/7508 A 0.75 1/3898 (0.0%) 0.70 2/5274 (0.0%)8 C 0.76 0/3900 0.75 2/5276 (0.0%)8 E 0.73 0/3876 0.70 3/5244 (0.1%)9 B 0.71 0/3676 0.71 5/4983 (0.1%)9 D 0.74 0/3693 0.69 2/5005 (0.0%)9 F 0.80 2/3684 (0.1%) 0.74 3/4994 (0.1%)All All 0.63 5/39620 (0.0%) 0.68 26/53694 (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 a

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


sidechain that are expected to be planar.

Mol Chain #Chirality outliers #Planarity outliers2 b 0 14 p 0 17 G 0 17 H 0 17 I 0 17 J 0 17 K 0 17 L 0 17 M 0 17 N 0 17 O 0 17 P 0 17 Q 0 17 R 0 17 S 0 17 T 0 18 A 0 28 C 0 38 E 0 29 D 0 1All All 0 24

All (5) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)9 F 276 PHE C-N -15.92 0.97 1.346 g 84 PRO N-CD 12.69 1.65 1.478 A 30 GLY C-N 8.21 1.52 1.344 p 105 ASP C-N -7.20 1.17 1.349 F 232 VAL CB-CG2 -6.69 1.38 1.52

All (26) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)8 C 30 GLY O-C-N -8.56 109.00 122.702 b 181 GLU O-C-N -8.07 109.79 122.708 E 30 GLY O-C-N -8.02 109.87 122.708 C 30 GLY C-N-CA 7.37 140.12 121.708 A 30 GLY O-C-N 6.64 133.32 122.709 B 273 ASP CB-CG-OD1 6.54 124.19 118.309 B 232 VAL CG1-CB-CG2 -5.71 101.77 110.90




Mol Chain Res Type Atoms Z Observed(o) Ideal(o)9 F 157 ASP CB-CG-OD2 5.27 123.04 118.309 B 157 ASP CB-CG-OD2 5.24 123.01 118.309 F 271 PHE O-C-N -5.21 114.36 122.706 g 248 ASP CB-CG-OD2 5.19 122.97 118.309 F 32 ASP CB-CG-OD2 5.18 122.96 118.301 a 186 LEU CB-CG-CD2 -5.17 102.20 111.009 D 32 ASP CB-CG-OD2 5.15 122.94 118.309 D 157 ASP CB-CG-OD2 5.12 122.91 118.301 a 229 LEU CA-CB-CG 5.12 127.07 115.306 g 220 LEU CB-CG-CD2 -5.11 102.31 111.008 A 345 LEU CB-CG-CD2 -5.11 102.31 111.006 g 241 ASP CB-CG-OD2 5.10 122.89 118.309 B 32 ASP CB-CG-OD2 5.10 122.89 118.306 g 264 LEU CA-CB-CG 5.08 126.99 115.308 E 230 ASP CB-CG-OD1 5.08 122.87 118.304 p 104 LEU CA-CB-CG 5.07 126.96 115.308 E 59 GLY N-CA-C 5.02 125.65 113.104 p 105 ASP C-N-CA -5.01 109.17 121.709 B 79 MET CG-SD-CE -5.01 92.18 100.20

There are no chirality outliers.

All (24) planarity outliers are listed below:

Mol Chain Res Type Group8 A 226 ALA Peptide8 A 262 ASP Peptide8 C 10 SER Peptide8 C 262 ASP Peptide8 C 30 GLY Mainchain9 D 273 ASP Peptide8 E 262 ASP Peptide8 E 30 GLY Mainchain7 G 77 ALA Mainchain7 H 77 ALA Mainchain7 I 77 ALA Mainchain7 J 77 ALA Mainchain7 K 77 ALA Mainchain7 L 77 ALA Mainchain7 M 77 ALA Mainchain7 N 77 ALA Mainchain7 O 77 ALA Mainchain7 P 77 ALA Mainchain




Mol Chain Res Type Group7 Q 77 ALA Mainchain7 R 77 ALA Mainchain7 S 77 ALA Mainchain7 T 77 ALA Mainchain2 b 181 GLU Mainchain4 p 105 ASP Mainchain

5.2 Too-close contacts iO

Due to software issues we are unable to calculate clashes - this section is therefore empty.

5.3 Torsion angles iO

5.3.1 Protein backbone iO

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 221/247 (90%) 211 (96%) 10 (4%) 0 100 100

2 b 157/184 (85%) 151 (96%) 6 (4%) 0 100 100

3 d 177/257 (69%) 170 (96%) 6 (3%) 1 (1%) 25 65

4 p 141/222 (64%) 130 (92%) 11 (8%) 0 100 100

5 e 129/134 (96%) 122 (95%) 7 (5%) 0 100 100

6 g 319/364 (88%) 306 (96%) 13 (4%) 0 100 100

7 G 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 H 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 I 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 J 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 K 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 L 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 M 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 N 77/81 (95%) 74 (96%) 3 (4%) 0 100 100Continued on next page...

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



Mol Chain Analysed Favoured Allowed Outliers Percentiles

7 O 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 P 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 Q 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 R 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 S 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

7 T 77/81 (95%) 74 (96%) 3 (4%) 0 100 100

8 A 499/507 (98%) 485 (97%) 14 (3%) 0 100 100

8 C 499/507 (98%) 478 (96%) 21 (4%) 0 100 100

8 E 496/507 (98%) 483 (97%) 13 (3%) 0 100 100

9 B 476/498 (96%) 444 (93%) 31 (6%) 1 (0%) 47 81

9 D 478/498 (96%) 463 (97%) 14 (3%) 1 (0%) 47 81

9 F 477/498 (96%) 463 (97%) 13 (3%) 1 (0%) 47 81

All All 5147/5557 (93%) 4942 (96%) 201 (4%) 4 (0%) 54 85

All (4) Ramachandran outliers are listed below:

Mol Chain Res Type3 d 217 LEU9 B 296 VAL9 F 296 VAL9 D 296 VAL

5.3.2 Protein sidechains iO

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 187/207 (90%) 187 (100%) 0 100 100

2 b 142/161 (88%) 142 (100%) 0 100 100

3 d 156/220 (71%) 156 (100%) 0 100 100

4 p 124/197 (63%) 124 (100%) 0 100 100Continued on next page...

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



Mol Chain Analysed Rotameric Outliers Percentiles

5 e 109/112 (97%) 109 (100%) 0 100 100

6 g 276/315 (88%) 276 (100%) 0 100 100

7 G 51/53 (96%) 51 (100%) 0 100 100

7 H 51/53 (96%) 51 (100%) 0 100 100

7 I 51/53 (96%) 51 (100%) 0 100 100

7 J 51/53 (96%) 51 (100%) 0 100 100

7 K 51/53 (96%) 51 (100%) 0 100 100

7 L 51/53 (96%) 51 (100%) 0 100 100

7 M 51/53 (96%) 51 (100%) 0 100 100

7 N 51/53 (96%) 51 (100%) 0 100 100

7 O 51/53 (96%) 51 (100%) 0 100 100

7 P 51/53 (96%) 51 (100%) 0 100 100

7 Q 51/53 (96%) 51 (100%) 0 100 100

7 R 51/53 (96%) 51 (100%) 0 100 100

7 S 51/53 (96%) 51 (100%) 0 100 100

7 T 51/53 (96%) 51 (100%) 0 100 100

8 A 410/414 (99%) 409 (100%) 1 (0%) 93 96

8 C 410/414 (99%) 410 (100%) 0 100 100

8 E 408/414 (99%) 408 (100%) 0 100 100

9 B 389/408 (95%) 388 (100%) 1 (0%) 92 95

9 D 391/408 (96%) 391 (100%) 0 100 100

9 F 390/408 (96%) 390 (100%) 0 100 100

All All 4106/4420 (93%) 4104 (100%) 2 (0%) 100 100

All (2) residues with a non-rotameric sidechain are listed below:

Mol Chain Res Type8 A 165 ARG9 B 278 PHE

Sometimes sidechains can be �ipped to improve hydrogen bonding and reduce clashes. All (62)such sidechains are listed below:


Mol Chain Res Type1 a 70 ASN1 a 86 GLN1 a 135 ASN1 a 193 ASN2 b 33 ASN2 b 133 GLN3 d 141 HIS3 d 188 ASN3 d 199 GLN3 d 240 GLN4 p 167 GLN4 p 195 GLN6 g 56 ASN6 g 81 ASN6 g 228 HIS6 g 301 ASN6 g 303 GLN7 S 42 GLN7 N 42 GLN7 O 42 GLN7 P 42 GLN7 Q 42 GLN7 R 42 GLN7 M 42 GLN7 T 42 GLN7 G 42 GLN7 H 42 GLN7 L 42 GLN7 K 42 GLN7 J 42 GLN7 I 42 GLN8 E 34 GLN8 E 43 HIS8 E 148 GLN8 E 208 GLN9 F 25 GLN9 F 238 GLN9 F 264 ASN9 F 280 GLN9 F 310 GLN9 F 384 HIS9 F 396 GLN8 A 28 ASN




Mol Chain Res Type8 A 66 ASN8 A 186 ASN8 A 187 GLN8 A 214 GLN8 A 256 HIS8 A 409 ASN8 A 423 GLN8 A 497 GLN9 B 71 ASN9 B 112 ASN9 B 210 ASN9 B 238 GLN9 B 345 HIS9 B 389 GLN8 C 187 GLN8 C 423 GLN9 D 67 GLN9 D 389 GLN9 D 396 GLN

5.3.3 RNA iO

There are no RNA molecules in this entry.

5.4 Non-standard residues in protein, DNA, RNA chains iO

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

5.5 Carbohydrates iO

There are no monosaccharides in this entry.

5.6 Ligand geometry iO

Of 10 ligands modelled in this entry, 5 are monoatomic - leaving 5 for Mogul analysis.

In the following table, the Counts columns list the number of bonds (or angles) for which Mogulstatistics could be retrieved, the number of bonds (or angles) that are observed in the model andthe number of bonds (or angles) that are de�ned in the Chemical Component Dictionary. TheLink column lists molecule types, if any, to which the group is linked. The Z score for a bondlength (or angle) is the number of standard deviations the observed value is removed from the

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_ligands


expected value. A bond length (or angle) with |Z| > 2 is considered an outlier worth inspection.RMSZ is the root-mean-square of all Z scores of the bond lengths (or angles).

Mol Type Chain Res LinkBond lengths Bond angles

Counts RMSZ #|Z| > 2 Counts RMSZ #|Z| > 210 ATP A 600 11 26,33,33 1.07 1 (3%) 31,52,52 1.36 4 (12%)

12 ADP D 600 11 24,29,29 1.32 3 (12%) 29,45,45 1.48 4 (13%)

10 ATP C 601 11 26,33,33 0.95 1 (3%) 31,52,52 1.52 6 (19%)

10 ATP E 600 11 26,33,33 1.19 2 (7%) 31,52,52 1.56 8 (25%)

12 ADP B 501 11 24,29,29 1.08 1 (4%) 29,45,45 1.48 4 (13%)

In the following table, the Chirals column lists the number of chiral outliers, the number of chiralcenters analysed, the number of these observed in the model and the number de�ned in theChemical Component Dictionary. Similar counts are reported in the Torsion and Rings columns.'-' means no outliers of that kind were identi�ed.

Mol Type Chain Res Link Chirals Torsions Rings10 ATP A 600 11 - 3/18/38/38 0/3/3/3

12 ADP D 600 11 - 5/12/32/32 0/3/3/310 ATP C 601 11 - 0/18/38/38 0/3/3/310 ATP E 600 11 - 4/18/38/38 0/3/3/3

12 ADP B 501 11 - 5/12/32/32 0/3/3/3

All (8) bond length outliers are listed below:

Mol Chain Res Type Atoms Z Observed(Å) Ideal(Å)12 D 600 ADP C2'-C1' -2.72 1.49 1.5310 E 600 ATP C2'-C1' -2.61 1.49 1.5312 B 501 ADP C2'-C1' -2.35 1.50 1.5312 D 600 ADP PB-O3B -2.23 1.46 1.5410 C 601 ATP C2'-C1' -2.13 1.50 1.5312 D 600 ADP O4'-C4' -2.06 1.40 1.4510 A 600 ATP C5-C4 2.06 1.46 1.4010 E 600 ATP PG-O2G -2.04 1.47 1.54

All (26) bond angle outliers are listed below:

Mol Chain Res Type Atoms Z Observed(o) Ideal(o)10 E 600 ATP N3-C2-N1 -3.93 122.53 128.6812 D 600 ADP N3-C2-N1 -3.87 122.63 128.6810 A 600 ATP N3-C2-N1 -3.49 123.22 128.6810 C 601 ATP N3-C2-N1 -3.44 123.30 128.68




Mol Chain Res Type Atoms Z Observed(o) Ideal(o)12 B 501 ADP C3'-C2'-C1' 3.30 105.94 100.9812 B 501 ADP N3-C2-N1 -3.25 123.60 128.6812 B 501 ADP PA-O3A-PB -3.24 121.69 132.8310 E 600 ATP C4-C5-N7 -3.18 106.08 109.4010 C 601 ATP C4-C5-N7 -2.66 106.62 109.4010 A 600 ATP O2B-PB-O1B 2.59 125.05 112.2410 E 600 ATP C2-N1-C6 2.53 123.09 118.7510 C 601 ATP C2-N1-C6 2.53 123.09 118.7512 D 600 ADP C4-C5-N7 -2.51 106.79 109.4010 C 601 ATP C3'-C2'-C1' 2.42 104.63 100.9810 E 600 ATP C3'-C2'-C1' 2.42 104.62 100.9812 B 501 ADP C4-C5-N7 -2.39 106.91 109.4012 D 600 ADP C2-N1-C6 2.33 122.75 118.7512 D 600 ADP O3B-PB-O2B 2.26 116.28 107.6410 C 601 ATP PB-O3B-PG -2.25 125.12 132.8310 A 600 ATP C2-N1-C6 2.24 122.58 118.7510 C 601 ATP C1'-N9-C4 -2.19 122.79 126.6410 E 600 ATP O2B-PB-O1B 2.17 122.98 112.2410 E 600 ATP PB-O3B-PG -2.11 125.59 132.8310 E 600 ATP C5'-C4'-C3' -2.07 107.43 115.1810 A 600 ATP O4'-C1'-C2' -2.04 103.95 106.9310 E 600 ATP O3B-PG-O1G -2.00 100.09 111.19

There are no chirality outliers.

All (17) torsion outliers are listed below:

Mol Chain Res Type Atoms12 B 501 ADP C5'-O5'-PA-O2A12 D 600 ADP C5'-O5'-PA-O1A12 D 600 ADP C5'-O5'-PA-O2A12 B 501 ADP O4'-C4'-C5'-O5'12 B 501 ADP C3'-C4'-C5'-O5'10 A 600 ATP PB-O3B-PG-O1G10 A 600 ATP PB-O3B-PG-O2G12 B 501 ADP C5'-O5'-PA-O3A10 E 600 ATP PG-O3B-PB-O2B10 E 600 ATP PA-O3A-PB-O2B12 D 600 ADP PB-O3A-PA-O2A12 B 501 ADP C5'-O5'-PA-O1A12 D 600 ADP O4'-C4'-C5'-O5'10 A 600 ATP PA-O3A-PB-O2B10 E 600 ATP PA-O3A-PB-O1B




Mol Chain Res Type Atoms12 D 600 ADP C5'-O5'-PA-O3A10 E 600 ATP PG-O3B-PB-O1B

There are no ring outliers.

No monomer is involved in short contacts.

The following is a two-dimensional graphical depiction of Mogul quality analysis of bond lengths,bond angles, torsion angles, and ring geometry for all instances of the Ligand of Interest. Inaddition, ligands with molecular weight > 250 and outliers as shown on the validation Tables willalso be included. For torsion angles, if less then 5% of the Mogul distribution of torsion angles iswithin 10 degrees of the torsion angle in question, then that torsion angle is considered an outlier.Any bond that is central to one or more torsion angles identi�ed as an outlier by Mogul will behighlighted in the graph. For rings, the root-mean-square deviation (RMSD) between the ringin question and similar rings identi�ed by Mogul is calculated over all ring torsion angles. If theaverage RMSD is greater than 60 degrees and the minimal RMSD between the ring in question andany Mogul-identi�ed rings is also greater than 60 degrees, then that ring is considered an outlier.The outliers are highlighted in purple. The color gray indicates Mogul did not �nd su�cientequivalents in the CSD to analyse the geometry.

Ligand ATP A 600

Bond lengths Bond angles

Torsions Rings


Ligand ADP D 600


Torsions Rings

Ligand ATP C 601


Torsions Rings


Ligand ATP E 600


Torsions Rings

Ligand ADP B 501


Torsions Rings


5.7 Other polymers iO

There are no such residues in this entry.

5.8 Polymer linkage issues iO

The following chains have linkage breaks:

Mol Chain Number of breaks4 p 12 b 19 F 1

All chain breaks are listed below:

Model Chain Residue-1 Atom-1 Residue-2 Atom-2 Distance (Å)1 b 77:GLN C 78:LEU N 2.251 p 105:ASP C 106:LYS N 1.171 F 276:PHE C 277:ARG N 0.97

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


6 Map visualisation iO

This section contains visualisations of the EMDB entry EMD-4272. These allow visual inspectionof the internal detail of the map and identi�cation of artifacts.

Images derived from a raw map, generated by summing the deposited half-maps, are presentedbelow the corresponding image components of the primary map to allow further visual inspectionand comparison with those of the primary map.

6.1 Orthogonal projections iO

6.1.1 Primary map

X Y Z

6.1.2 Raw map

X Y Z

The images above show the map projected in three orthogonal directions.

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


6.2 Central slices iO

6.2.1 Primary map

X Index: 175 Y Index: 175 Z Index: 175

6.2.2 Raw map


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

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


6.3 Largest variance slices iO

6.3.1 Primary map


6.3.2 Raw map


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

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


6.4 Orthogonal surface views iO

6.4.1 Primary map

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.05.These images, in conjunction with the slice images, may facilitate assessment of whether an ap-propriate contour level has been provided.

6.4.2 Raw map

X Y Z

These images show the 3D surface of the raw map. The raw map's contour level was selected sothat its surface encloses the same volume as the primary map does at its recommended contourlevel.

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


6.5 Mask visualisation iO

This section shows the 3D surface view of the primary map at 50% transparency overlaid with thespeci�ed 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_4272_msk_1.map iO

X Y Z

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


7 Map analysis iO

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

7.1 Map-value distribution iO

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 iO

The volume at the recommended contour level is 269 nm3; this corresponds to an approximatemass of 243 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 iO

*Reported resolution corresponds to spatial frequency of 0.233 Å−1

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


8 Fourier-Shell correlation iO

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-o� and 0.5 cut-o�.

8.1 FSC iO

*Reported resolution corresponds to spatial frequency of 0.233 Å−1

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


8.2 Resolution estimates iO

Resolution estimate (Å)Estimation criterion (FSC cut-o�)0.143 0.5 Half-bit

Reported by author 4.30 - -Author-provided FSC curve 4.39 7.00 4.45

Calculated* 7.78 11.25 8.14

*Resolution estimate based on FSC curve calculated by comparison of deposited half-maps. Thevalue from deposited half-maps intersecting FSC 0.143 CUT-OFF 7.78 di�ers from the reportedvalue 4.3 by more than 10 %

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


9 Map-model �t iO

This section contains information regarding the �t between EMDB map EMD-4272 and PDBmodel 6FKI. Per-residue inclusion information can be found in section 3 on page 8.

9.1 Map-model overlay iO

X Y Z

The images above show the 3D surface view of the map at the recommended contour level 0.05 at50% 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 �t 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 iO

At the recommended contour level, 74% of all backbone atoms, 56% 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 mapRaw map

Central slicesPrimary mapRaw map

Largest variance slicesPrimary mapRaw map

Orthogonal surface viewsPrimary mapRaw map

Mask visualisationemd_4272_msk_1.map

Map analysisMap-value distributionVolume estimateRotationally averaged power spectrum

Fourier-Shell correlationFSCResolution estimates

Map-model fitMap-model overlayAtom inclusion

Documents

Full wwPDB EM Validation Report O i - RCSB...Ideal geometry (DNA, RNA) : Parkinson et al. (1996) alidationV Pipeline (wwPDB-VP) : 2.15.1 Page 2 ullF wwPDB EM alidationV Report EMD-4272,