Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9797 Å / Relative weight: 1
Reflection
Resolution: 3→50 Å / Num. obs: 47393 / % possible obs: 99.2 % / Redundancy: 6.9 % / Rsym value: 0.074 / Net I/σ(I): 14.83
Reflection shell
Resolution: 3→3.18 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.114 / Mean I/σ(I) obs: 1.58 / % possible all: 95.5
-
Processing
Software
Name
Version
Classification
PHENIX
1.9_1692
refinement
XDS
datareduction
XDS
datascaling
SHARP
phasing
Coot
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 3→47.898 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.85 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2576
2363
4.99 %
Rwork
0.2161
-
-
obs
0.2182
47386
99.23 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 3→47.898 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7736
0
64
14
7814
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
7905
X-RAY DIFFRACTION
f_angle_d
1.04
10655
X-RAY DIFFRACTION
f_dihedral_angle_d
12.664
3019
X-RAY DIFFRACTION
f_chiral_restr
0.046
1228
X-RAY DIFFRACTION
f_plane_restr
0.004
1366
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.9956-3.0567
0.4636
130
0.4687
2292
X-RAY DIFFRACTION
88
3.0567-3.1232
0.4616
127
0.3771
2655
X-RAY DIFFRACTION
100
3.1232-3.1958
0.4081
143
0.3172
2705
X-RAY DIFFRACTION
100
3.1958-3.2757
0.3256
138
0.2854
2631
X-RAY DIFFRACTION
100
3.2757-3.3642
0.296
141
0.27
2694
X-RAY DIFFRACTION
100
3.3642-3.4632
0.3548
141
0.2617
2669
X-RAY DIFFRACTION
100
3.4632-3.575
0.3216
140
0.2582
2667
X-RAY DIFFRACTION
100
3.575-3.7027
0.3145
139
0.2302
2650
X-RAY DIFFRACTION
100
3.7027-3.8509
0.2748
141
0.2173
2689
X-RAY DIFFRACTION
100
3.8509-4.0261
0.245
140
0.2215
2688
X-RAY DIFFRACTION
100
4.0261-4.2382
0.3169
137
0.2118
2654
X-RAY DIFFRACTION
100
4.2382-4.5035
0.2809
139
0.1868
2676
X-RAY DIFFRACTION
100
4.5035-4.851
0.1653
145
0.1673
2678
X-RAY DIFFRACTION
100
4.851-5.3386
0.2707
138
0.1844
2658
X-RAY DIFFRACTION
100
5.3386-6.1097
0.25
141
0.2231
2665
X-RAY DIFFRACTION
100
6.1097-7.6924
0.2631
140
0.2304
2673
X-RAY DIFFRACTION
100
7.6924-47.9043
0.2014
143
0.1933
2679
X-RAY DIFFRACTION
100
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
2.8794
-0.1605
-1.7083
0.359
-0.2529
1.8479
0.0016
-0.2541
-0.5863
-0.0969
-0.0948
-0.1355
0.1894
0.8217
0.0029
0.6121
-0.1121
0.0224
0.7811
0.015
0.6939
-4.9709
-31.9816
-47.3711
2
0.5471
0.2191
-1.0706
1.7824
1.2329
3.1496
0.5732
-0.2154
-0.18
-0.8914
0.2791
-0.098
-1.1327
-1.1267
0.9197
1.2624
0.1561
0.204
0.5215
-0.0106
0.667
-21.9846
-14.4947
-73.6009
3
1.9987
-0.068
-0.3155
1.9334
0.5842
2.7178
0.0771
0.0576
-0.5108
0.07
-0.1899
0.1811
0.3649
-0.2482
0.0006
0.5933
-0.2006
0.0072
0.5975
0.0795
0.7099
-25.5311
-37.2568
-43.0775
4
1.5261
-0.7398
1.1891
0.9754
-1.0706
1.42
0.2914
0.4079
0.4639
-0.1211
-0.2067
0.0975
-0.6727
-0.7016
-0.0451
0.9878
0.2891
0.3534
0.7612
0.3838
0.8662
-42.1269
-2.3945
-30.1092
5
-0.7742
-0.3748
-1.9732
2.7457
2.6447
-0.3493
0.4761
0.0132
-0.0072
0.0616
0.104
-0.6988
0.0861
0.5949
0.5305
0.8814
-0.4505
-0.0021
0.866
0.0592
0.9236
-12.7075
-2.7489
-21.9558
6
1.2715
0.1393
-0.7676
0.9496
-0.2808
0.5103
0.5195
-0.1075
-0.2707
-0.0884
-0.226
0.551
-0.2103
-0.6847
0.0191
0.707
-0.235
0.1415
0.7107
0.0578
0.768
-32.0167
-21.9146
-18.5859
7
0.0908
0.1939
0.1928
0.7519
0.8041
0.8419
0.3188
0.9319
-0.1651
0.0101
0.2999
1.3577
0.9947
-0.704
-0.0707
0.6428
0.0066
-0.0519
1.1963
0.1532
0.8401
-49.7608
-21.0638
-27.7444
8
0.6867
-0.4027
-0.4031
0.2484
0.2229
0.2147
-0.426
0.9705
1.4264
-1.6905
0.9855
-0.55
-0.7059
-0.4429
-0.0027
1.4477
-0.4449
-0.1111
1.1977
-0.2054
1.0515
-24.5312
-25.5171
-79.1862
9
3.2564
0.1232
0.7724
0.0279
0.0038
0.7691
-0.2275
0.4179
0.6964
0.7647
-0.104
-1.6937
-0.255
0.1863
0.0532
1.4603
-0.068
-0.0046
0.5348
-0.1867
1.0461
-15.027
-22.3294
-82.4854
10
0.0673
0.0447
0.0687
0.074
0.0361
0.0522
0.9627
0.1404
-0.1443
-0.1078
0.8062
-0.3416
-0.0537
0.5454
0.0017
1.7163
0.2259
0.3405
1.4247
-0.2037
1.3025
-5.4943
-18.5616
-72.608
11
2.956
-1.4686
0.8504
1.1098
-0.0572
0.6669
0.0212
1.1081
-0.223
-0.8742
0.2063
-0.8138
-0.6998
0.9457
-0.0052
0.7274
-0.3068
0.2142
0.7311
-0.4562
1.6527
-5.0109
-19.595
-91.3752
12
0.4922
0.202
-0.1504
0.1461
-0.1026
0.0677
-0.986
0.3371
-0.6191
-1.0627
-1.0203
-0.0971
-0.1023
0.2572
-0.0215
1.6847
-0.4965
0.0299
3.0119
-0.4487
1.3565
-10.5267
-20.5029
-111.06
13
0.6015
0.0072
-0.3166
0.0331
-0.0484
0.1719
-0.7108
0.1287
-1.5694
0.5418
-0.0916
0.1463
0.4505
-0.3824
-0.6099
2.1739
-0.4789
-0.0078
1.1952
0.0554
1.4716
-13.4625
-27.5636
-94.8256
14
2.7591
0.7002
2.6943
4.6049
2.8032
3.6785
1.0752
0.4915
0.1626
1.7726
0.5745
1.0483
-0.0598
-1.8376
1.9349
0.972
-0.2199
0.3966
1.6733
0.1915
1.0013
-15.6124
13.6714
-8.1814
15
0.3616
0.3403
-0.125
0.1572
0.5647
0.1405
0.1395
-0.3449
0.6446
0.0645
0.3849
0.5559
0.2212
-0.0546
0.117
0.4899
0.0412
0.261
1.1013
-0.3606
1.5572
-19.7811
21.8506
-8.987
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid2through153 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid154through1208 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid1209through1311 )
4
X-RAY DIFFRACTION
4
chain 'B' and (resid2through153 )
5
X-RAY DIFFRACTION
5
chain 'B' and (resid154through1227 )
6
X-RAY DIFFRACTION
6
chain 'B' and (resid1228through1290 )
7
X-RAY DIFFRACTION
7
chain 'B' and (resid1291through1312 )
8
X-RAY DIFFRACTION
8
chain 'C' and (resid438through451 )
9
X-RAY DIFFRACTION
9
chain 'C' and (resid452through471 )
10
X-RAY DIFFRACTION
10
chain 'C' and (resid472through476 )
11
X-RAY DIFFRACTION
11
chain 'C' and (resid477through495 )
12
X-RAY DIFFRACTION
12
chain 'C' and (resid496through504 )
13
X-RAY DIFFRACTION
13
chain 'C' and (resid505through531 )
14
X-RAY DIFFRACTION
14
chain 'D' and (resid439through471 )
15
X-RAY DIFFRACTION
15
chain 'D' and (resid472through524 )
+
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