Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.965459 Å / Relative weight: 1
Reflection
Resolution: 2.687→33.726 Å / Num. obs: 23452 / % possible obs: 91.6 % / Redundancy: 6.1 % Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary! CC1/2: 0.998 / CC1/2 anomalous: -0.362 / Rmerge(I) obs: 0.0717 / Rpim(I) all: 0.0316 / Rrim(I) all: 0.0785 / AbsDiff over sigma anomalous: 0.692 / Baniso tensor eigenvalue 1: 23.0769 Å2 / Baniso tensor eigenvalue 2: 18.3309 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 0.8302 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.5575 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.5575 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.8302 / Aniso diffraction limit 1: 2.977 Å / Aniso diffraction limit 2: 2.734 Å / Aniso diffraction limit 3: 2.68 Å / Aniso diffraction limit axis 1 ortho1: 0.90037 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.43509 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.43509 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.90037 / Net I/σ(I): 13.96 / Num. measured all: 143017 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 91 / % possible ellipsoidal: 91.6 / % possible ellipsoidal anomalous: 91 / % possible spherical: 81.6 / % possible spherical anomalous: 81 / Redundancy anomalous: 3.15 / Signal type: local
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. measured obs
Num. unique all
Num. unique obs
CC1/2
CC1/2 anomalous
Rpim(I) all
Rrim(I) all
AbsDiff over sigma anomalous
% possible anomalous
% possible ellipsoidal
% possible ellipsoidal anomalous
% possible spherical
% possible spherical anomalous
Redundancy anomalous
% possible all
6.248-33.726
5.48
0.0325
34.85
12847
12847
2344
2344
0.998
-0.477
0.0146
0.0357
0.607
99.2
99.2
99.2
99.2
99.2
2.93
99.2
4.94-6.248
6.11
0.049
29.15
14329
14329
2346
2346
0.996
-0.416
0.0215
0.0537
0.665
99.7
100
99.7
100
99.7
3.18
100
4.315-4.94
5.68
0.0536
25.72
13312
13312
2345
2345
0.996
-0.224
0.0247
0.0592
0.715
99.4
99.7
99.4
99.7
99.4
2.95
99.7
3.915-4.315
5.99
0.0797
19.15
14048
14048
2345
2345
0.995
-0.233
0.0355
0.0875
0.715
99
100
99
100
99
3.12
100
3.631-3.915
6.39
0.135
12.72
14994
14994
2346
2346
0.99
-0.107
0.058
0.1471
0.717
99.6
99.9
99.6
99.9
99.6
3.28
99.9
3.416-3.631
6.52
0.2328
7.84
15287
15287
2344
2344
0.975
-0.005
0.0988
0.2533
0.716
99.7
99.9
99.7
99.9
99.7
3.35
99.9
3.242-3.416
6.66
0.4044
4.63
15606
15606
2345
2345
0.935
0.026
0.1693
0.4389
0.705
99.8
100
99.8
100
99.8
3.41
100
3.101-3.242
6.29
0.6814
2.6
14767
14767
2347
2347
0.82
0.003
0.2951
0.7438
0.687
99.8
100
99.8
100
99.8
3.23
100
2.975-3.101
5.81
1.0483
1.57
13623
13623
2344
2344
0.644
0.021
0.4759
1.1539
0.702
95.5
95.7
95.5
95.7
95.5
2.98
95.7
2.687-2.975
6.05
1.2206
1.34
14204
14204
2346
2346
0.547
0.004
0.5414
1.3377
0.688
53.1
53.7
53.1
31.3
31.1
3.1
53.7
-
Processing
Software
Name
Version
Classification
autoPROC
1.1.720220608
dataprocessing
XDS
Jan10, 2022
datareduction
Aimless
0.7.9
datascaling
STARANISO
2.3.87
datascaling
REFMAC
5.8.0352
refinement
REFMAC
5.8.0352
phasing
Refinement
Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.687→33.726 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.917 / SU B: 37.351 / SU ML: 0.351 / Cross valid method: FREE R-VALUE / ESU R Free: 0.412 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2533
1194
5.091 %
Rwork
0.1951
22258
-
all
0.198
-
-
obs
-
23452
81.564 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 98.219 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.476 Å2
-0 Å2
-1.306 Å2
2-
-
0.87 Å2
-0 Å2
3-
-
-
1.816 Å2
Refinement step
Cycle: LAST / Resolution: 2.687→33.726 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6708
0
56
89
6853
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.003
0.012
6914
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.016
6432
X-RAY DIFFRACTION
r_angle_refined_deg
0.812
1.653
9361
X-RAY DIFFRACTION
r_angle_other_deg
0.283
1.571
14984
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.225
5
818
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
3.283
5
40
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.885
10
1248
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
13.013
10
320
X-RAY DIFFRACTION
r_chiral_restr
0.037
0.2
1055
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
7650
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1357
X-RAY DIFFRACTION
r_nbd_refined
0.187
0.2
1428
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.175
0.2
6370
X-RAY DIFFRACTION
r_nbtor_refined
0.174
0.2
3345
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.074
0.2
3681
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.137
0.2
165
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.007
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.106
0.2
9
X-RAY DIFFRACTION
r_nbd_other
0.116
0.2
46
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.038
0.2
2
X-RAY DIFFRACTION
r_mcbond_it
2.538
7.01
3302
X-RAY DIFFRACTION
r_mcbond_other
2.536
7.011
3302
X-RAY DIFFRACTION
r_mcangle_it
4.367
10.498
4110
X-RAY DIFFRACTION
r_mcangle_other
4.367
10.498
4111
X-RAY DIFFRACTION
r_scbond_it
2.151
7.2
3612
X-RAY DIFFRACTION
r_scbond_other
2.151
7.201
3613
X-RAY DIFFRACTION
r_scangle_it
3.72
10.709
5251
X-RAY DIFFRACTION
r_scangle_other
3.72
10.71
5252
X-RAY DIFFRACTION
r_lrange_it
6.767
81.749
7704
X-RAY DIFFRACTION
r_lrange_other
6.766
81.74
7703
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.687-2.756
0.502
5
0.268
75
X-RAY DIFFRACTION
3.8204
2.756-2.831
0.264
24
0.371
318
X-RAY DIFFRACTION
16.6019
2.831-2.913
0.417
55
0.336
847
X-RAY DIFFRACTION
45.88
2.913-3.002
0.34
72
0.307
1437
X-RAY DIFFRACTION
78.5528
3.002-3.099
0.335
92
0.286
1734
X-RAY DIFFRACTION
97.5949
3.099-3.207
0.252
88
0.264
1761
X-RAY DIFFRACTION
100
3.207-3.327
0.333
99
0.246
1634
X-RAY DIFFRACTION
100
3.327-3.461
0.294
90
0.231
1617
X-RAY DIFFRACTION
99.9415
3.461-3.614
0.287
75
0.217
1531
X-RAY DIFFRACTION
99.9378
3.614-3.788
0.235
80
0.194
1483
X-RAY DIFFRACTION
99.9361
3.788-3.99
0.272
68
0.188
1434
X-RAY DIFFRACTION
99.9335
3.99-4.228
0.216
75
0.163
1292
X-RAY DIFFRACTION
99.9269
4.228-4.515
0.227
66
0.166
1255
X-RAY DIFFRACTION
99.6229
4.515-4.87
0.218
62
0.165
1172
X-RAY DIFFRACTION
99.8382
4.87-5.323
0.236
53
0.182
1094
X-RAY DIFFRACTION
100
5.323-5.933
0.223
66
0.189
961
X-RAY DIFFRACTION
100
5.933-6.816
0.241
47
0.204
885
X-RAY DIFFRACTION
99.8928
6.816-8.264
0.225
34
0.179
748
X-RAY DIFFRACTION
98.8622
8.264-11.352
0.197
24
0.144
606
X-RAY DIFFRACTION
98.9011
11.352-33.726
0.399
19
0.214
374
X-RAY DIFFRACTION
99.7462
Refinement TLS params.
Method: refined / Origin x: 32.5494 Å / Origin y: -1.1008 Å / Origin z: 25.9238 Å
11
12
13
21
22
23
31
32
33
T
0.2863 Å2
-0.0196 Å2
0.0763 Å2
-
0.0091 Å2
-0.0094 Å2
-
-
0.0507 Å2
L
3.7308 °2
0.6721 °2
0.6408 °2
-
0.5783 °2
0.1366 °2
-
-
1.3675 °2
S
-0.0485 Å °
-0.0078 Å °
-0.2724 Å °
0.0036 Å °
0.058 Å °
-0.0859 Å °
-0.2369 Å °
0.021 Å °
-0.0095 Å °
Refinement TLS group
Selection: ALL
+
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