Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9786 Å / Relative weight: 1
Reflection
Resolution: 2.504→73.027 Å / Num. obs: 7248 / % possible obs: 85.5 % / Redundancy: 8.11 % 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: 0.999 / CC1/2 anomalous: -0.069 / Rmerge(I) obs: 0.0691 / Rpim(I) all: 0.0258 / Rrim(I) all: 0.0741 / AbsDiff over sigma anomalous: 0.779 / Baniso tensor eigenvalue 1: 86.5 Å2 / Baniso tensor eigenvalue 2: 86.5 Å2 / Baniso tensor eigenvalue 3: 68.8 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.704 Å / Aniso diffraction limit 2: 2.704 Å / Aniso diffraction limit 3: 2.413 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / 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 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 18.44 / Num. measured all: 58812 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 83.2 / % possible ellipsoidal: 85.5 / % possible ellipsoidal anomalous: 83.2 / % possible spherical: 75.7 / % possible spherical anomalous: 73.2 / Redundancy anomalous: 4.33 / 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
7.458-73.027
6.97
0.0285
51.19
2682
2682
385
385
0.999
-0.113
0.011
0.0307
0.725
91
96
91
96
91
4.09
96
5.93-7.458
7.7
0.0397
40.14
2873
2873
373
373
0.999
0.056
0.0148
0.0426
0.755
95.9
99.2
95.9
99.2
95.9
4.26
99.2
5.167-5.93
7.72
0.0462
37.4
2888
2888
374
374
0.998
-0.04
0.0174
0.0496
0.816
97.2
100
97.2
100
97.2
4.2
100
4.696-5.167
8.12
0.0445
39.48
2990
2990
368
368
0.999
-0.04
0.0165
0.0477
0.726
97.5
99.7
97.5
99.7
97.5
4.38
99.7
4.358-4.696
7.94
0.0484
35.58
2890
2890
364
364
0.999
0.105
0.0182
0.052
0.778
97.5
100
97.5
100
97.5
4.25
100
4.103-4.358
8.03
0.0559
33.1
2963
2963
369
369
0.998
-0.123
0.0209
0.0599
0.784
97.6
100
97.6
100
97.6
4.28
100
3.894-4.103
7.72
0.075
26.84
2849
2849
369
369
0.997
-0.033
0.0292
0.0809
0.812
97.6
100
97.6
100
97.6
4.14
100
3.724-3.894
8.12
0.0918
23.02
2916
2916
359
359
0.995
-0.028
0.0345
0.0984
0.831
98.2
100
98.2
100
98.2
4.27
100
3.578-3.724
8.12
0.1318
18.79
2933
2933
361
361
0.989
-0.134
0.0494
0.1414
0.79
98.2
100
98.2
100
98.2
4.28
100
3.363-3.578
7.84
0.1809
13.41
2917
2917
372
372
0.989
0.057
0.0683
0.1942
0.772
53.7
54.9
53.7
54.9
53.7
4.19
54.9
3.264-3.363
7.93
0.254
9.56
2880
2880
363
363
0.978
0.025
0.0954
0.2722
0.869
97
99.7
97
99.7
97
4.2
99.7
3.18-3.264
8.16
0.3274
7.36
2938
2938
360
360
0.961
-0.057
0.121
0.3502
0.768
96.1
99.7
96.1
99.7
96.1
4.34
99.7
3.1-3.18
8.29
0.402
6.25
2984
2984
360
360
0.964
0.053
0.1474
0.4294
0.775
97
99.7
97
99.7
97
4.38
99.7
3.028-3.1
7.66
0.4554
4.95
2774
2774
362
362
0.933
-0.06
0.1731
0.4887
0.779
96.7
100
96.7
100
96.7
4.07
100
2.965-3.028
8.08
0.5988
3.68
2860
2860
354
354
0.901
-0.058
0.2206
0.6399
0.786
97.5
100
97.5
100
97.5
4.28
100
2.905-2.965
8.27
0.7717
2.82
2951
2951
357
357
0.833
-0.027
0.2818
0.8241
0.79
97
100
97
100
97
4.33
100
2.851-2.905
8.37
0.874
2.52
2963
2963
354
354
0.801
-0.029
0.3159
0.9315
0.734
96.1
97.8
96.1
97.8
96.1
4.39
97.8
2.793-2.851
8.69
0.9844
2.24
3024
3024
348
348
0.768
0.088
0.3488
1.0468
0.78
87.8
88.8
87.8
88.8
87.8
4.52
88.8
2.734-2.793
9.43
1.0827
2.13
3263
3263
346
346
0.698
0.03
0.3681
1.1449
0.791
75.3
74.9
75.3
74.9
75.3
4.85
74.9
2.504-2.734
9.35
1.5137
1.42
3274
3274
350
350
0.559
-0.11
0.5169
1.602
0.704
31.5
32.6
31.5
16.1
15.2
4.99
32.6
-
Processing
Software
Name
Version
Classification
BUSTER
2.11.8
refinement
autoPROC
dataprocessing
XDS
jan10, 2022
datareduction
STARANISO
2.3.77
datascaling
PHASER
2.8.3
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: In house structure Resolution: 2.504→73.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / SU R Blow DPI: 3.057 / SU Rfree Blow DPI: 0.321
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2395
363
-
RANDOM
Rwork
0.2052
-
-
-
obs
0.2069
7248
75.8 %
-
Displacement parameters
Biso mean: 77.83 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.7349 Å2
0 Å2
0 Å2
2-
-
0.7349 Å2
0 Å2
3-
-
-
-1.4697 Å2
Refine analyze
Luzzati coordinate error obs: 0.38 Å
Refinement step
Cycle: LAST / Resolution: 2.504→73.03 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1761
0
23
26
1810
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.008
1824
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
0.93
2469
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
648
SINUSOIDAL
2
X-RAY DIFFRACTION
t_gen_planes
341
HARMONIC
5
X-RAY DIFFRACTION
t_it
1813
HARMONIC
10
X-RAY DIFFRACTION
t_chiral_improper_torsion
240
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_ideal_dist_contact
1471
SEMIHARMONIC
4
X-RAY DIFFRACTION
t_omega_torsion
2.46
X-RAY DIFFRACTION
t_other_torsion
20.42
LS refinement shell
Resolution: 2.504→2.74 Å
Rfactor
Num. reflection
% reflection
Rfree
0.2015
18
-
Rwork
0.2832
-
-
obs
-
-
17.95 %
+
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