PolycombproteinEED / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic ...hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1
Mass: 42227.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal glycine left after TEV cleavage / Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli (E. coli) / References: UniProt: O75530
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.8→48.58 Å / Num. obs: 67617 / % possible obs: 95.1 % / Redundancy: 6.63 % 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: -0.011 / Rmerge(I) obs: 0.1012 / Rpim(I) all: 0.0423 / Rrim(I) all: 0.1098 / AbsDiff over sigma anomalous: 0.747 / Baniso tensor eigenvalue 1: 37.9 Å2 / Baniso tensor eigenvalue 2: 16.6 Å2 / Baniso tensor eigenvalue 3: 17.6 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: 2.095 Å / Aniso diffraction limit 2: 1.759 Å / Aniso diffraction limit 3: 1.722 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): 12.55 / Num. measured all: 448284 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 94.8 / % possible ellipsoidal: 95.1 / % possible ellipsoidal anomalous: 94.8 / % possible spherical: 85.7 / % possible spherical anomalous: 85.2 / Redundancy anomalous: 3.48 / 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
5.284-48.58
6.52
0.0401
35.47
22058
22058
3381
3381
0.999
-0.027
0.0169
0.0436
0.865
100
99.8
100
99.8
100
3.73
99.8
4.16-5.284
5.87
0.0361
36.02
19855
19855
3380
3380
0.999
0.013
0.0162
0.0397
0.775
99.9
99.8
99.9
99.8
99.9
3.19
99.8
3.617-4.16
6.58
0.0444
32.1
22256
22256
3382
3382
0.999
-0.086
0.0187
0.0483
0.771
99.9
100
99.9
100
99.9
3.5
100
3.28-3.617
6.8
0.0564
27
22968
22968
3380
3380
0.999
0.018
0.0233
0.0611
0.792
99.6
100
99.6
100
99.6
3.61
100
3.038-3.28
6.92
0.077
21.25
23384
23384
3381
3381
0.997
0.015
0.0314
0.0833
0.804
99.1
100
99.1
100
99.1
3.65
100
2.855-3.038
7.04
0.106
16.18
23788
23788
3380
3380
0.996
-0.025
0.0428
0.1144
0.759
100
100
100
100
100
3.7
100
2.709-2.855
6.95
0.133
13.05
23503
23503
3381
3381
0.993
0.016
0.054
0.1437
0.769
100
100
100
100
100
3.65
100
2.588-2.709
6.34
0.1685
9.9
21443
21443
3382
3382
0.988
0.003
0.0723
0.1837
0.764
100
100
100
100
100
3.34
100
2.488-2.588
6.07
0.1942
8.37
20538
20538
3381
3381
0.982
-0.003
0.0858
0.2128
0.753
99.9
99.9
99.9
99.9
99.9
3.19
99.9
2.399-2.488
6.38
0.232
7.41
21575
21575
3380
3380
0.978
-0.045
0.0996
0.2529
0.735
99.7
100
99.7
100
99.7
3.33
100
2.323-2.399
6.64
0.2642
6.76
22431
22431
3379
3379
0.98
0.013
0.1102
0.2866
0.739
99.8
100
99.8
100
99.8
3.45
100
2.255-2.323
6.76
0.301
6.06
22881
22881
3383
3383
0.973
-0.006
0.1241
0.3259
0.725
99.9
99.9
99.9
99.9
99.9
3.51
99.9
2.193-2.255
6.88
0.3357
5.63
23276
23276
3381
3381
0.967
-0.023
0.1371
0.3629
0.725
97.9
97.8
97.9
97.8
97.9
3.57
97.8
2.135-2.193
6.9
0.3389
5.54
23333
23333
3381
3381
0.969
0.041
0.1376
0.3662
0.72
92.9
92.5
92.9
92.5
92.9
3.57
92.5
2.08-2.135
6.92
0.3828
4.9
23380
23380
3381
3381
0.96
-0.012
0.1552
0.4135
0.703
89.1
88.5
89.1
88.3
88.9
3.57
88.5
2.027-2.08
6.96
0.4405
4.28
23516
23516
3380
3380
0.949
-0.016
0.1782
0.4756
0.728
89.6
89.4
89.6
83.2
84
3.59
89.4
1.976-2.027
6.93
0.4943
3.88
23414
23414
3381
3381
0.933
0.009
0.1999
0.5338
0.734
91.7
91.7
91.7
77.1
77.8
3.58
91.7
1.902-1.976
6.76
0.6023
3.07
22857
22857
3380
3380
0.871
-0.015
0.2456
0.6513
0.706
64.4
65.4
64.4
47.9
47.4
3.53
65.4
1.852-1.902
6.14
0.7378
2.26
20756
20756
3382
3382
0.832
-0.03
0.3188
0.8056
0.688
96.3
97.9
96.3
60.8
60.3
3.22
97.9
1.8-1.852
6.23
0.9048
1.89
21072
21072
3381
3381
0.714
-0.019
0.3897
0.987
0.716
97.9
98.1
97.9
53.3
53.3
3.22
98.1
-
Processing
Software
Name
Version
Classification
autoPROC
1.1.720210420
dataprocessing
autoPROC
Jan31, 2020
dataprocessing
STARANISO
0.7.7
datascaling
autoPROC
2.3.73
dataprocessing
BUSTER
2.11.8
refinement
autoPROC
datareduction
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H19
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