Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97918 Å / Relative weight: 1
Reflection
Resolution: 1.8→44.7 Å / Num. obs: 171175 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rsym value: 0.09 / Net I/σ(I): 23.3
Reflection shell
Resolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.99 / % possible all: 99.9
-
Processing
Software
Name
Version
Classification
PHENIX
dev_1951
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.8→36.936 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.19 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1997
2054
2.3 %
Random Selection
Rwork
0.169
-
-
-
obs
0.1697
171157
99.39 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.8→36.936 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5200
0
0
717
5917
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
5579
X-RAY DIFFRACTION
f_angle_d
1.119
7635
X-RAY DIFFRACTION
f_dihedral_angle_d
13.18
2061
X-RAY DIFFRACTION
f_chiral_restr
0.057
882
X-RAY DIFFRACTION
f_plane_restr
0.004
977
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.8-1.8206
0.3356
134
0.2976
5882
X-RAY DIFFRACTION
97
1.8206-1.8436
0.2775
139
0.3
5947
X-RAY DIFFRACTION
99
1.8436-1.8679
0.3013
144
0.2815
6016
X-RAY DIFFRACTION
100
1.8679-1.8935
0.2527
147
0.2628
5949
X-RAY DIFFRACTION
100
1.8935-1.9205
0.2357
139
0.252
6045
X-RAY DIFFRACTION
100
1.9205-1.9492
0.3224
152
0.2384
5962
X-RAY DIFFRACTION
100
1.9492-1.9796
0.2556
147
0.2347
5962
X-RAY DIFFRACTION
100
1.9796-2.0121
0.2112
128
0.2169
6036
X-RAY DIFFRACTION
100
2.0121-2.0468
0.2788
156
0.205
5994
X-RAY DIFFRACTION
100
2.0468-2.084
0.2089
130
0.1971
6000
X-RAY DIFFRACTION
100
2.084-2.1241
0.2431
156
0.1927
5935
X-RAY DIFFRACTION
100
2.1241-2.1674
0.2227
135
0.1821
5987
X-RAY DIFFRACTION
100
2.1674-2.2146
0.2141
130
0.1834
6012
X-RAY DIFFRACTION
100
2.2146-2.2661
0.2357
143
0.1785
5986
X-RAY DIFFRACTION
100
2.2661-2.3227
0.2011
153
0.1793
6015
X-RAY DIFFRACTION
100
2.3227-2.3855
0.185
143
0.1769
5950
X-RAY DIFFRACTION
100
2.3855-2.4557
0.2119
141
0.1768
5986
X-RAY DIFFRACTION
100
2.4557-2.5349
0.2072
143
0.1695
6018
X-RAY DIFFRACTION
100
2.5349-2.6255
0.1905
142
0.1639
6021
X-RAY DIFFRACTION
100
2.6255-2.7306
0.1951
142
0.161
5993
X-RAY DIFFRACTION
100
2.7306-2.8548
0.2001
139
0.1654
5982
X-RAY DIFFRACTION
100
2.8548-3.0053
0.3245
140
0.1746
6002
X-RAY DIFFRACTION
100
3.0053-3.1935
0.1661
148
0.1653
5986
X-RAY DIFFRACTION
100
3.1935-3.4399
0.1839
137
0.1541
5912
X-RAY DIFFRACTION
99
3.4399-3.7858
0.1699
132
0.1416
5897
X-RAY DIFFRACTION
98
3.7858-4.3328
0.1638
144
0.1269
5961
X-RAY DIFFRACTION
99
4.3328-5.4561
0.1355
129
0.1264
5879
X-RAY DIFFRACTION
98
5.4561-36.9442
0.2075
128
0.1834
5901
X-RAY DIFFRACTION
98
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
3.4567
-0.5385
0.8933
2.1277
-1.1694
3.4769
0.1154
-0.1695
-0.4218
0.0008
-0.0235
0.0635
0.1731
-0.1755
-0.1105
0.1625
0.0198
-0.0125
0.2419
-0.0015
0.2636
36.7411
70.4489
105.4835
2
2.9364
-0.5952
-0.9506
0.6045
0.02
1.3321
0.1296
0.4451
-0.0066
-0.0532
-0.0526
0.1044
-0.0199
-0.1935
-0.0617
0.2298
0.0917
-0.016
0.354
-0.0082
0.223
35.8689
83.6807
90.229
3
0.8004
-0.1539
1.1294
1.1791
-0.8823
2.7105
0.2981
0.9364
0.2724
-0.5717
-0.3724
0.3557
-0.1771
-0.3657
-0.1259
0.3914
0.1681
-0.0132
0.6765
0.0924
0.3495
46.07
91.4674
77.622
4
2.7898
0.7048
-0.8706
1.4622
-1.0619
1.3677
0.1142
-0.1336
-0.1955
0.1047
-0.1801
-0.1228
-0.0961
0.2431
0.0473
0.2084
0.0423
-0.0257
0.3025
-0.0139
0.21
56.4422
76.1677
101.4058
5
1.6775
-0.0256
0.682
2.3868
-1.7767
3.4367
-0.0481
0.1596
-0.0523
-0.3791
0.22
0.2654
0.3084
-0.3212
-0.1452
0.2776
-0.0918
-0.0346
0.2183
0.0216
0.247
44.2723
57.9839
47.1116
6
1.4371
0.8679
0.1063
3.7207
0.1547
1.9065
0.1225
-0.1524
-0.3054
0.0901
-0.0946
-0.3191
0.1944
0.0372
-0.0725
0.1806
0.008
0.0148
0.173
0.0396
0.2436
58.2
53.3188
65.3707
7
1.5563
0.7071
1.1842
1.8058
0.1066
1.0147
-0.2262
0.3506
0.1333
-0.2889
0.155
0.0336
-0.2647
0.3061
0.0419
0.287
-0.0985
0.0139
0.3025
0.015
0.2223
58.1199
73.6447
51.1529
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid3through84 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid85through200 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid201through236 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid237through369 )
5
X-RAY DIFFRACTION
5
chain 'B' and (resid5through84 )
6
X-RAY DIFFRACTION
6
chain 'B' and (resid85through236 )
7
X-RAY DIFFRACTION
7
chain 'B' and (resid237through369 )
+
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