Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.986 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2235
2915
5 %
RANDOM
Rwork
0.1771
-
-
-
all
0.17941
55952
-
-
obs
0.17941
55376
98.97 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 26.303 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.9 Å2
0 Å2
0 Å2
2-
-
-3.47 Å2
0 Å2
3-
-
-
2.57 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→10 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4773
0
46
539
5358
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.019
4895
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
4751
X-RAY DIFFRACTION
r_angle_refined_deg
1.348
1.976
6636
X-RAY DIFFRACTION
r_angle_other_deg
0.764
3
10900
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.285
5
617
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.698
24.159
226
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.358
15
853
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.694
15
44
X-RAY DIFFRACTION
r_chiral_restr
0.083
0.2
762
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
5553
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1075
X-RAY DIFFRACTION
r_rigid_bond_restr
2.555
3
9646
X-RAY DIFFRACTION
r_sphericity_free
37.127
5
147
X-RAY DIFFRACTION
r_sphericity_bonded
10.933
5
9964
LS refinement shell
Resolution: 1.8→1.845 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.288
207
-
Rwork
0.236
3940
-
obs
-
-
99.74 %
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
6.7828
1.6143
-1.0156
0.468
-0.3678
0.3459
-0.019
0.0957
0.0857
-0.0153
0.0567
0.0525
0.0186
-0.0649
-0.0377
0.1533
-0.0028
0.0022
0.1634
-0.0112
0.1172
-28.0898
-8.7556
7.5683
2
3.597
-1.4694
0.6132
1.0492
-0.4218
0.3425
0.0327
0.0032
-0.1782
0.0289
0.0011
0.0139
0.0769
0.0201
-0.0338
0.1425
-0.0001
-0.0074
0.1445
-0.0008
0.0458
-5.5312
-9.763
11.0077
3
0.8393
0.0799
0.3482
1.7808
-0.1291
0.8266
0.0094
-0.0992
-0.0373
0.1111
-0.0239
-0.1334
0.0432
0.0438
0.0144
0.1445
0.0002
-0.0158
0.1637
0.0196
0.087
4.7132
-13.104
21.8031
4
2.3993
-0.4236
0.4208
0.789
-0.191
1.497
0.033
-0.0138
-0.056
0.0631
-0.0144
0.1826
0.0331
-0.0336
-0.0186
0.1528
-0.0017
-0.0005
0.1543
0.0013
0.0546
-8.4009
-9.9584
21.497
5
2.5001
0.7192
1.2805
1.7619
-0.5969
1.2585
0.0386
-0.0428
0.07
0.2532
-0.0828
0.0335
-0.1175
0.0379
0.0442
0.2005
-0.0109
0.0116
0.1947
0.0104
0.0708
2.1022
-9.2765
27.6972
6
0.2047
0.0057
0.232
0.2291
0.2028
0.4446
0.046
0.0164
-0.0519
0.0242
0.0228
-0.0546
0.028
0.0569
-0.0688
0.1766
-0.0119
-0.0231
0.1958
0.0335
0.1284
5.7798
-4.9101
20.809
7
0.4889
0.4348
-0.9833
3.4917
-0.9917
1.985
0.0341
-0.016
-0.0268
0.1074
-0.1046
-0.4834
-0.0991
0.0443
0.0705
0.1639
-0.0059
-0.0395
0.1826
0.0073
0.1263
12.8324
0.2552
22.6241
8
0.4585
0.2931
-0.2015
0.2047
-0.0449
0.563
-0.0329
-0.0254
-0.0879
-0.0325
-0.0077
-0.067
0.0396
0.0578
0.0406
0.1663
-0
0.0083
0.1701
0.0077
0.0916
3.4576
-0.244
11.6291
9
1.728
0.5998
-0.5433
4.7973
1.303
1.3421
-0.0556
0.0623
0.0492
-0.1385
-0.0142
-0.4116
0.007
0.0701
0.0699
0.158
-0.0048
-0.0038
0.1737
0.0223
0.1197
8.6388
15.0571
9.0669
10
0.1842
0.1246
-0.3421
2.4308
-0.8373
0.7927
0.01
0.0031
-0.0071
0.1099
-0.041
-0.0761
-0.0495
-0.0058
0.031
0.1591
-0.0051
-0.0062
0.164
-0.0029
0.0739
-4.4582
12.2952
17.2487
11
0.4054
-0.485
-0.0123
1.4128
-0.134
0.0857
-0.0157
-0.0342
0.0703
0.0814
-0.0019
-0.0757
-0.0472
0.0419
0.0177
0.162
-0.0091
-0.0092
0.1653
-0.0053
0.0811
-0.8108
21.1737
16.2471
12
0.3788
-0.0609
-0.1691
2.062
-0.3374
0.4772
-0.0089
-0.0022
0.0612
0.0423
0.0322
0.1242
-0.0312
-0.0132
-0.0233
0.1506
-0.0029
-0.0009
0.1462
0.0024
0.0621
-10.6032
14.3075
10.0863
13
0.3276
-0.2532
-0.0988
1.4855
0.8894
0.5442
-0.0134
0.0108
0.0225
-0.0236
-0.0216
0.0427
-0.008
0.0024
0.035
0.1677
0.0003
0.0034
0.1652
0.0038
0.0787
-5.9692
22.7643
5.1728
14
1.1713
0.3153
0.291
0.4189
0.4682
0.5457
-0.01
0.1085
0.1011
-0.0148
-0.0086
0.0558
-0.0086
-0.0261
0.0185
0.1386
0.0008
-0.0045
0.1472
0.0103
0.089
-16.1245
2.7477
5.8475
15
1.6228
0.0804
0.1018
0.9408
-0.1964
0.1956
-0.0275
-0.0659
0.0628
0.0738
-0.0117
0.1536
0.0082
-0.0251
0.0393
0.1543
-0.0017
0.0015
0.1569
-0.0155
0.0651
-23.7945
0.4161
15.5683
16
1.4173
0.053
0.0259
1.1086
0.2308
2.3599
-0.0117
-0.1649
-0.006
0.1299
-0.013
0.212
0.047
-0.1768
0.0247
0.1325
-0.0107
-0.0245
0.1541
-0.0011
0.0713
-32.822
-8.5611
20.185
17
2.073
1.066
-0.1517
0.9404
0.0913
0.2926
0.0075
0.0009
-0.1272
0.0145
-0.0231
0.0332
0.0442
-0.0182
0.0157
0.1487
0.0007
0.0024
0.1532
-0.0035
0.0679
-20.4935
-11.5721
13.5861
18
1.4287
1.1411
-1.4659
1.4039
-2.0422
3.2472
-0.0634
0.0384
0.032
-0.0656
0.0456
0.0301
0.2306
-0.0144
0.0178
0.1474
0.0119
-0.0088
0.1339
-0.0209
0.0955
-27.652
-11.5877
7.8703
19
3.0902
0.5122
1.6163
0.0963
0.3165
1.0603
0.0393
0.0883
-0.1016
0.0115
0.0199
-0.0142
0.0632
0.0634
-0.0593
0.1653
-0.0071
0.0028
0.1622
0.0027
0.0601
-3.4143
-7.4474
2.338
20
13.6748
2.0602
-7.7466
0.456
-0.8086
5.7006
-0.2275
0.1916
0.2447
-0.074
0.0077
0.0302
0.0535
-0.0395
0.2198
0.1499
0.0284
0.0033
0.2227
0.0983
0.324
9.0388
-13.3801
8.1239
21
5.0322
-0.5916
-0.9865
0.1307
0.206
0.3313
-0.007
-0.1083
-0.0106
0.0245
0.0353
-0.0363
0.0311
0.0573
-0.0283
0.1597
0.0123
-0.0006
0.1684
0.0088
0.1217
23.5106
-8.8609
-8.024
22
0.7533
0.331
0.179
0.5281
0.3014
0.4415
0.0012
0.0368
-0.038
-0.0436
-0.0263
0.005
0.0612
-0.0142
0.0251
0.1474
0.0032
-0.0043
0.1513
-0.0024
0.061
-1.4426
-11.1789
-17.5783
23
5.1875
-2.7543
1.9894
1.4639
-1.0114
3.7879
0.0013
-0.1525
0.0041
0.013
0.1141
-0.0045
0.2374
-0.0341
-0.1154
0.1829
0.0024
-0.0076
0.2001
-0.0235
0.064
-1.265
-17.8181
-25.304
24
0.0536
0.0954
0.1033
0.2506
0.172
0.2075
0.002
0.0007
0.0178
-0.0569
-0.0255
0.0503
0.0192
-0.0267
0.0235
0.1698
0.0008
-0.0035
0.175
-0.0051
0.0824
-10.3277
-6.3653
-24.5526
25
2.5234
2.6493
-0.1737
2.9912
0.2355
0.851
-0.1275
-0.0078
0.1576
-0.0966
-0.0387
0.2632
0.0328
-0.0487
0.1662
0.1788
0.0162
0.0053
0.1711
-0.0054
0.1227
-16.5934
2.2137
-20.2938
26
1.6216
0.654
1.2208
0.423
0.363
1.1085
-0.0108
-0.0608
0.0213
-0.0007
-0.0091
0.0894
0.0069
-0.0805
0.0199
0.1555
0.0015
0.002
0.1652
-0.0054
0.098
-11.679
-4.1712
-15.7263
27
4.0177
-2.0053
-0.655
5.2049
-0.6983
0.3654
0.0302
-0.2479
0.1749
0.1832
0.0372
0.1881
-0.031
0.0476
-0.0674
0.1582
-0.0059
0.0194
0.1647
-0.0357
0.1276
-11.2148
11.8286
-8.6554
28
0.1991
0.3899
-0.1073
1.0434
0.0085
0.2307
0.0179
0.0122
0.0167
-0.037
-0.029
0.0571
-0.0558
-0.0326
0.0111
0.1617
0.0098
-0.0051
0.166
0.0018
0.0877
-1.7422
13.2227
-16.7576
29
1.4945
-2.342
-0.0072
5.1305
-0.5349
0.2212
0.0514
0.1432
0.0134
-0.0587
-0.0081
0.1708
-0.0305
-0.0569
-0.0433
0.1656
0.0054
-0.0121
0.1819
0.0094
0.1012
-11.1439
14.8206
-17.9374
30
0.1103
0.0562
-0.1111
1.1814
0.1549
0.3243
0.0206
0.0244
0.0571
-0.0481
-0.0026
0.001
-0.0557
-0.0108
-0.0181
0.1588
0.0051
0.0057
0.1522
0.0042
0.0787
2.0025
19.6987
-13.496
31
0.5594
-0.5501
0.522
1.3293
-1.1798
1.0621
-0.028
-0.0078
-0.0005
0.0397
-0.0208
-0.0828
-0.0461
-0.0204
0.0489
0.1592
0.0015
0.0023
0.173
-0.0027
0.0858
1.1973
22.7399
-5.3055
32
0.2987
0.2106
-0.1096
0.7435
-0.7562
0.8184
0.0128
-0.0981
0.0235
0.0235
-0.0238
-0.0005
-0.0142
0.0036
0.011
0.1374
-0.0027
-0.0025
0.1383
-0.0044
0.0515
9.2473
2.9881
-6.2163
33
2.3277
-1.1371
-2.9651
2.0319
0.6159
4.3866
0.0812
-0.1847
0.1413
-0.1127
0.0881
-0.0891
-0.0093
0.0995
-0.1693
0.1416
-0.0138
-0.0066
0.1684
0.0041
0.108
24.8866
0.0558
-8.0574
34
1.8842
0.7977
-0.2989
1.431
0.4187
0.3478
0.0047
0.1045
0.0647
-0.1086
0.0211
-0.0964
-0.0176
-0.0001
-0.0258
0.1648
0.0083
0.0246
0.167
0.0209
0.0939
14.4334
-0.013
-17.1868
35
0.5783
0.1704
-0.0339
2.8273
0.883
0.5152
-0.0259
0.0669
0.1279
-0.046
0.0186
-0.0396
0.0104
0.0447
0.0073
0.1484
0.0021
0.0111
0.1651
0.0109
0.0781
21.7499
-0.1128
-17.7254
36
2.6102
0.1485
1.1366
1.3078
0.3627
2.771
-0.0257
0.2454
0.0204
-0.0839
0.0187
-0.1966
0.011
0.1603
0.007
0.1615
-0.0024
0.0114
0.1486
0.013
0.0767
28.9086
-8.6564
-20.6984
37
0.6949
-0.9532
-0.0823
1.3125
0.1012
0.0588
0.005
-0.0021
-0.0219
-0.0115
-0.0009
0.0183
0.0219
0.0173
-0.0041
0.1498
-0.002
-0.0009
0.153
-0.0031
0.0906
15.8118
-11.6371
-13.8479
38
1.6511
-1.5372
-1.8433
1.8936
1.974
3.1154
-0.1184
-0.0695
-0.0313
0.0401
0.0296
-0.0388
0.1499
0.0836
0.0888
0.1471
-0.008
-0.0164
0.1471
0.0235
0.0886
22.9846
-11.7078
-8.2966
39
5.0209
0.9314
2.2394
0.1866
0.3693
1.1787
0.0221
-0.0845
-0.0568
-0.0114
-0.019
-0.0261
0.1046
-0.0762
-0.0031
0.1634
0.0053
-0.0133
0.1619
-0.0002
0.0647
-2.0694
-7.7974
-3.1256
40
12.7145
6.3928
5.1829
9.7073
5.0846
11.4436
-0.092
-0.3579
0.4339
0.5957
-0.8193
0.4014
0.6317
-0.4779
0.9113
0.2374
-0.0023
0.0421
0.1973
-0.0254
0.075
-12.3754
-15.6408
-7.5751
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 7
2
X-RAY DIFFRACTION
2
A
8 - 24
3
X-RAY DIFFRACTION
3
A
25 - 37
4
X-RAY DIFFRACTION
4
A
38 - 49
5
X-RAY DIFFRACTION
5
A
50 - 64
6
X-RAY DIFFRACTION
6
A
65 - 77
7
X-RAY DIFFRACTION
7
A
78 - 89
8
X-RAY DIFFRACTION
8
A
90 - 103
9
X-RAY DIFFRACTION
9
A
104 - 114
10
X-RAY DIFFRACTION
10
A
115 - 127
11
X-RAY DIFFRACTION
11
A
128 - 162
12
X-RAY DIFFRACTION
12
A
163 - 181
13
X-RAY DIFFRACTION
13
A
182 - 193
14
X-RAY DIFFRACTION
14
A
194 - 210
15
X-RAY DIFFRACTION
15
A
211 - 246
16
X-RAY DIFFRACTION
16
A
247 - 261
17
X-RAY DIFFRACTION
17
A
262 - 280
18
X-RAY DIFFRACTION
18
A
281 - 297
19
X-RAY DIFFRACTION
19
A
298 - 304
20
X-RAY DIFFRACTION
20
A
305 - 309
21
X-RAY DIFFRACTION
21
B
1 - 7
22
X-RAY DIFFRACTION
22
B
8 - 49
23
X-RAY DIFFRACTION
23
B
50 - 54
24
X-RAY DIFFRACTION
24
B
55 - 76
25
X-RAY DIFFRACTION
25
B
77 - 86
26
X-RAY DIFFRACTION
26
B
87 - 100
27
X-RAY DIFFRACTION
27
B
101 - 112
28
X-RAY DIFFRACTION
28
B
113 - 127
29
X-RAY DIFFRACTION
29
B
128 - 140
30
X-RAY DIFFRACTION
30
B
141 - 181
31
X-RAY DIFFRACTION
31
B
182 - 193
32
X-RAY DIFFRACTION
32
B
194 - 207
33
X-RAY DIFFRACTION
33
B
208 - 216
34
X-RAY DIFFRACTION
34
B
217 - 235
35
X-RAY DIFFRACTION
35
B
236 - 248
36
X-RAY DIFFRACTION
36
B
249 - 261
37
X-RAY DIFFRACTION
37
B
262 - 280
38
X-RAY DIFFRACTION
38
B
281 - 297
39
X-RAY DIFFRACTION
39
B
298 - 305
40
X-RAY DIFFRACTION
40
B
306 - 310
+
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