Monochromator: DOUBLE SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97976 Å / Relative weight: 1
Reflection
Resolution: 2.72→40.33 Å / Num. obs: 76488 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.56 % / Biso Wilson estimate: 47.96 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.88
Reflection shell
Resolution: 2.71→2.78 Å / Redundancy: 2.93 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.11 / % possible all: 89.5
-
Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
XDS
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.714→41.849 Å / SU ML: 0.8 / σ(F): 1.99 / Phase error: 27.85 / Stereochemistry target values: ML / Details: FRIEDEL'S MATES HAVE BEEN MERGED.
Rfactor
Num. reflection
% reflection
Rfree
0.261
1989
5 %
Rwork
0.1996
-
-
obs
0.2027
39553
99.12 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.039 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Biso mean: 58 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-11.268 Å2
0 Å2
-3.5913 Å2
2-
-
1.272 Å2
0 Å2
3-
-
-
9.9959 Å2
Refinement step
Cycle: LAST / Resolution: 2.714→41.849 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11182
0
50
80
11312
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
11490
X-RAY DIFFRACTION
f_angle_d
1.236
15674
X-RAY DIFFRACTION
f_dihedral_angle_d
14.402
3990
X-RAY DIFFRACTION
f_chiral_restr
0.076
1822
X-RAY DIFFRACTION
f_plane_restr
0.005
1996
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Refine-ID
Type
1
1
A
X-RAY DIFFRACTION
POSITIONAL
1
2
B
X-RAY DIFFRACTION
POSITIONAL
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.7144-2.7822
0.349
133
0.243
2453
X-RAY DIFFRACTION
92
2.7822-2.8575
0.3007
133
0.2318
2679
X-RAY DIFFRACTION
100
2.8575-2.9415
0.3204
127
0.226
2690
X-RAY DIFFRACTION
100
2.9415-3.0364
0.316
145
0.2198
2709
X-RAY DIFFRACTION
100
3.0364-3.1449
0.2961
135
0.2081
2705
X-RAY DIFFRACTION
100
3.1449-3.2708
0.3125
147
0.2117
2676
X-RAY DIFFRACTION
100
3.2708-3.4196
0.2688
173
0.2054
2663
X-RAY DIFFRACTION
100
3.4196-3.5998
0.3071
150
0.2272
2665
X-RAY DIFFRACTION
99
3.5998-3.8252
0.2967
135
0.219
2710
X-RAY DIFFRACTION
99
3.8252-4.1203
0.2665
127
0.193
2645
X-RAY DIFFRACTION
98
4.1203-4.5345
0.2027
142
0.1536
2741
X-RAY DIFFRACTION
100
4.5345-5.1896
0.2038
134
0.1582
2723
X-RAY DIFFRACTION
100
5.1896-6.5343
0.2587
143
0.2004
2734
X-RAY DIFFRACTION
100
6.5343-41.8542
0.2193
165
0.2062
2771
X-RAY DIFFRACTION
99
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
4.2603
0.5661
-0.1693
2.9068
0.4317
3.3418
0.1218
-0.075
-0.2461
-0.153
0.0946
0.1919
-0.2403
-0.0413
-0.187
0.331
-0.0469
0.0237
0.2367
-0.0053
0.3122
99.4678
44.2393
6.9373
2
1.7788
0.7035
-0.256
1.5739
-0.6454
1.3926
0.0597
-0.1439
0.241
0.1523
-0.0199
-0.1833
-0.1773
-0.0216
-0.0378
0.2872
0.0073
-0.0271
0.2806
-0.0271
0.3595
102.908
40.2491
9.2643
3
3.0535
0.881
-0.7861
0.3578
0.4039
0.6722
0.1365
0.1292
0.7775
-0.1322
-0.0789
0.2668
-0.3258
-0.222
-0.0417
0.4386
0.0713
-0.1128
0.3265
0.0085
0.5344
75.8289
41.8391
12.9448
4
2.0483
0.6748
0.0326
2.1708
-0.3537
0.868
0.1673
-0.7208
0.3731
0.6668
-0.2044
0.3499
-0.2238
-0.0811
0.0192
0.5345
-0.0663
0.0689
0.5865
-0.1242
0.3206
70.0778
30.566
42.5058
5
2.1693
0.8599
0.0519
1.1738
0.2834
2.9821
0.0048
-0.044
-0.8165
-0.0366
-0.0005
-0.5155
0.4054
0.255
0.0448
0.437
0.084
0.0287
0.326
-0.0039
0.9521
107.1322
-1.1343
13.7032
6
2.3579
0.3634
-0.1122
1.099
-0.0385
0.6725
0.0602
-0.0559
-0.365
0.1743
-0.0904
0.0549
0.1566
-0.133
0.026
0.3608
-0.019
-0.0064
0.2899
-0.0446
0.2349
73.8691
13.1693
21.4003
7
2.3952
0.0542
0.4729
2.5637
0.4545
1.2441
0.0085
0.3389
-0.4226
-0.0016
0.0485
0.0791
0.2679
0.0107
-0.0371
0.265
-0.0234
0.0219
0.4173
-0.1092
0.3439
64.3921
9.0352
14.5192
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINAAND (RESSEQ6:65)
2
X-RAY DIFFRACTION
2
CHAINAAND (RESSEQ66:289)
3
X-RAY DIFFRACTION
3
CHAINAAND (RESSEQ290:363)
4
X-RAY DIFFRACTION
4
CHAINAAND (RESSEQ364:808)
5
X-RAY DIFFRACTION
5
CHAINBAND (RESSEQ5:188)
6
X-RAY DIFFRACTION
6
CHAINBAND (RESSEQ189:607)
7
X-RAY DIFFRACTION
7
CHAINBAND (RESSEQ608:808)
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi