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→46.73 Å / Num. obs: 61524 / % possible obs: 96.7 % / Redundancy: 7.79 % 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 through the data processing procedure (rejection of overloaded or too partial reflections, outlier/misfit rejection 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 / Rmerge(I) obs: 0.1267 / Rpim(I) all: 0.0476 / Rrim(I) all: 0.1356 / Net I/σ(I): 11.16 / Num. measured all: 479342
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
Rpim(I) all
Rrim(I) all
% possible all
4.75-46.73
7.25
0.0456
31.89
33507
33507
4622
4622
0.999
0.0178
0.0491
100
3.793-4.75
7.14
0.0486
29.87
30416
30416
4261
4261
0.999
0.0191
0.0523
100
3.338-3.793
7.76
0.068
24.15
31182
31182
4020
4020
0.998
0.0255
0.0728
100
3.043-3.338
7.94
0.0918
18.29
31828
31828
4008
4008
0.997
0.0341
0.0981
100
2.832-3.043
8.01
0.1337
13.03
31757
31757
3965
3965
0.995
0.0496
0.1428
100
2.674-2.832
7.67
0.1805
9.66
29257
29257
3812
3812
0.99
0.0688
0.1934
100
2.551-2.674
7.31
0.2297
7.45
26900
26900
3678
3678
0.983
0.09
0.2472
100
2.448-2.551
7.06
0.2761
6.15
25683
25683
3636
3636
0.974
0.1103
0.298
99.8
2.362-2.448
7.61
0.3453
5.23
26177
26177
3439
3439
0.969
0.1319
0.3701
96.1
2.286-2.362
7.84
0.3992
4.79
25222
25222
3216
3216
0.955
0.1493
0.4267
93.3
2.221-2.286
8
0.4435
4.55
24351
24351
3043
3043
0.95
0.1642
0.4735
95.6
2.162-2.221
8.1
0.4674
4.33
22973
22973
2837
2837
0.95
0.1713
0.4984
95.7
2.11-2.162
8.3
0.5275
3.89
21155
21155
2548
2548
0.942
0.1905
0.5615
94.3
2.063-2.11
8.28
0.6229
3.35
19200
19200
2318
2318
0.907
0.2243
0.6629
93.1
2.018-2.063
8.31
0.6556
3.19
18408
18408
2214
2214
0.918
0.2364
0.6977
93
1.978-2.018
8.32
0.8194
2.68
17004
17004
2044
2044
0.838
0.294
0.8717
95.3
1.937-1.978
8.42
1.0098
2.13
16532
16532
1964
1964
0.805
0.3601
1.0733
93
1.897-1.937
8.4
1.0451
2.02
16206
16206
1929
1929
0.767
0.3697
1.11
91.5
1.852-1.897
7.99
1.2742
1.58
15956
15956
1996
1996
0.701
0.4642
1.3585
90.7
1.8-1.852
7.92
1.5159
1.31
15628
15628
1974
1974
0.584
0.5571
1.6177
86.4
-
Processing
Software
Name
Version
Classification
autoPROC
1.1.720200918
dataprocessing
autoPROC
Jan31, 2020
dataprocessing
STARANISO
0.7.7
datascaling
autoPROC
2.3.46
dataprocessing
BUSTER
2.11.7
refinement
autoPROC
datareduction
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H19
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