Resolution: 3→94.77 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.908 / SU B: 66.07 / SU ML: 0.518 / Cross valid method: THROUGHOUT / ESU R Free: 0.539 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29625
823
5 %
RANDOM
Rwork
0.24961
-
-
-
obs
0.25196
15488
94.26 %
-
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: 118.623 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.03 Å2
-0 Å2
0 Å2
2-
-
-3.93 Å2
-0 Å2
3-
-
-
3.9 Å2
Refinement step
Cycle: LAST / Resolution: 3→94.77 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5290
0
0
0
5290
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.019
5415
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
4879
X-RAY DIFFRACTION
r_angle_refined_deg
1.027
1.948
7353
X-RAY DIFFRACTION
r_angle_other_deg
0.701
3
11304
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.458
5
684
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.436
24.292
233
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.889
15
899
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.239
15
31
X-RAY DIFFRACTION
r_chiral_restr
0.059
0.2
819
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
6153
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
1220
X-RAY DIFFRACTION
r_mcbond_it
1.885
7.348
2754
X-RAY DIFFRACTION
r_mcbond_other
1.884
7.348
2753
X-RAY DIFFRACTION
r_mcangle_it
3.252
11.016
3432
X-RAY DIFFRACTION
r_mcangle_other
3.252
11.016
3433
X-RAY DIFFRACTION
r_scbond_it
1.57
7.505
2661
X-RAY DIFFRACTION
r_scbond_other
1.567
7.505
2659
X-RAY DIFFRACTION
r_scangle_other
2.714
11.19
3921
X-RAY DIFFRACTION
r_long_range_B_refined
5.484
57.218
5738
X-RAY DIFFRACTION
r_long_range_B_other
5.484
57.221
5739
LS refinement shell
Resolution: 3→3.078 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.378
58
-
Rwork
0.366
1111
-
obs
-
-
93.45 %
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
5.366
-0.5989
6.6135
0.0932
-0.7495
8.2772
-0.4684
1.3364
0.7336
0.0394
-0.2118
-0.0448
-0.4491
1.7423
0.6802
0.5045
-0.0952
0.0046
0.5292
-0.086
0.7518
-9.2427
21.1868
-38.0014
2
21.9364
7.7999
9.9575
2.8104
3.5903
4.6543
-0.1798
0.1914
-0.2007
-0.1794
0.1132
0.0152
-0.3214
0.0254
0.0666
0.5934
-0.0154
-0.1733
0.2825
-0.0019
0.4009
-30.5461
24.2251
-47.0688
3
26.7339
-4.1406
-1.0035
0.7311
0.4308
0.9035
0.3016
0.8114
0.6153
-0.0332
-0.1328
-0.1227
0.106
-0.0598
-0.1687
0.5522
-0.075
-0.0256
0.0393
0.004
0.3262
-20.7928
17.9772
-46.2186
4
2.4572
-2.5898
-1.8063
8.8343
2.4656
1.5408
-0.0032
-0.8028
-0.4036
-1.1736
-0.0271
0.7976
-0.0842
0.4914
0.0303
0.5146
0.037
-0.1196
0.4183
0.1068
0.534
-16.4342
12.8607
-37.1836
5
5.6641
-3.6314
-1.3223
15.8855
14.0182
13.1671
0.6877
0.2098
-0.584
-1.461
-1.0515
0.7901
-1.0517
-1.0278
0.3638
0.4353
0.0497
-0.2712
0.2915
0.2774
0.5985
-30.0368
17.553
-31.8605
6
14.3994
-2.6516
7.577
2.3183
2.3804
11.8534
0.0418
-0.1682
-0.3387
-0.0618
0.005
0.1812
0.0354
-0.0887
-0.0468
0.4702
-0.0026
-0.1518
0.1111
-0.018
0.3102
-18.0773
4.5888
-40.8575
7
7.4507
5.7789
8.5901
8.8978
5.1583
10.431
0.2538
-0.5577
0.0761
-0.1907
-0.0078
1.1856
0.4866
-0.8197
-0.246
0.5218
-0.0995
-0.0689
0.4237
0.0923
0.7385
-33.2936
8.2667
-37.7809
8
24.8956
-4.1515
-12.0596
6.6886
0.4586
6.2535
0.2877
-0.466
0.8022
-0.1905
0.2207
0.3906
-0.1476
0.178
-0.5084
0.4265
-0.0825
-0.1279
0.0957
0.0099
0.11
-18.9926
11.7816
-45.9045
9
7.5313
-4.1711
3.1682
5.8671
-1.4927
3.5683
-0.3781
0.0028
0.024
0.1029
0.2832
0.3244
-0.2163
0.0512
0.0949
0.3345
-0.102
0.0451
0.0561
0.0234
0.0751
-22.9201
14.9135
-36.3456
10
5.9307
-5.2346
1.9223
5.7531
-1.9928
1.8837
0.2526
-0.4018
-0.4776
-0.7673
0.174
0.5768
0.3106
-0.5129
-0.4265
0.4895
-0.0562
-0.0382
0.2483
0.0592
0.1276
-26.3296
24.6614
-39.2673
11
7.0453
2.4633
-3.8472
14.9923
24.6488
49.9601
-0.1703
-0.2604
-0.1002
-0.5317
-0.5667
0.403
-0.7782
-0.752
0.737
0.5685
0.0725
-0.0877
0.2584
0.0721
0.3825
-42.9927
51.5949
-35.9876
12
17.9255
-9.9711
-11.1301
11.015
1.6548
10.676
0.0945
-1.4453
0.9533
0.3782
0.5511
-0.4827
-0.4197
1.0809
-0.6456
0.4976
-0.0026
0.0331
0.4618
0.0061
0.3903
-37.8374
58.695
-19.1465
13
15.9925
-3.755
6.6158
3.4535
-5.5603
8.9888
0.9307
-0.1299
-0.2796
-0.3351
-0.1057
0.5128
0.6069
0.0987
-0.825
0.4145
-0.1981
0.0679
0.4337
0.1201
0.3782
-40.7408
47.6681
-35.0566
14
5.192
-5.249
-1.1183
9.4407
-2.3267
3.1441
-0.0635
0.4612
-1.0014
0.3088
-0.6702
0.3992
-0.0957
0.059
0.7337
0.6663
-0.1303
-0.0282
0.1496
-0.0034
0.3296
-33.7865
39.3313
-41.227
15
3.0633
0.8765
-2.3612
12.9082
-8.0598
8.8779
-0.0427
-0.1504
-0.1618
-0.0661
0.302
0.1021
-0.1887
0.7898
-0.2593
0.3448
-0.0219
0.0156
0.3275
-0.0232
0.2189
-30.1475
50.1469
-30.6948
16
10.7246
0.617
8.2658
0.631
-0.4099
7.7031
-0.3576
0.0031
0.0625
0.1257
0.5757
0.21
-0.4181
-0.8908
-0.2181
0.6288
0.0096
-0.0057
0.653
0.0557
0.4431
-41.0989
36.0339
-37.9904
17
1.8051
0.5895
0.5319
19.666
10.5944
5.7462
0.366
-0.799
0.4322
-0.1587
-0.4696
0.0027
-0.0639
-0.3255
0.1036
0.5807
-0.0419
0.1284
0.444
-0.0645
0.3303
-34.5955
55.9014
-25.773
18
1.231
-1.1061
1.6416
1.029
-1.5024
2.2146
-0.2033
0.0573
0.2417
0.2147
-0.0145
-0.0871
-0.3335
0.0708
0.2179
0.5671
-0.0318
0.0391
0.3099
0.0682
0.5595
-35.5481
62.2746
-31.631
19
8.0504
6.8694
4.2211
13.5024
0.3172
3.6521
-0.1035
0.2823
0.1366
-0.4018
-0.0881
-0.0572
-0.0256
0.3357
0.1916
0.6003
-0.0111
-0.0917
0.3077
0.1169
0.1928
-31.3195
45.6443
-45.1814
20
8.7345
-6.9012
-4.1346
7.0856
4.7315
3.306
0.5315
0.0631
0.5994
-0.1005
-0.5155
-0.0821
-0.0123
-0.5543
-0.0159
0.5529
0.0511
-0.0078
0.4587
0.1504
0.472
-41.4269
57.9211
-37.0243
21
0.4472
4.0734
0.7397
47.0538
10.3396
2.5633
0.1309
0.1104
-0.0159
0.1238
-0.836
1.749
-0.0726
-0.5285
0.7051
0.4175
0.1274
-0.0667
0.659
-0.1829
0.6378
-30.0215
13.2478
-18.4898
22
16.2782
-7.5048
1.9704
5.4548
2.8834
7.4757
-0.4288
-0.7679
0.1797
0.4133
0.2571
0.0185
0.3461
-0.1969
0.1716
0.5975
0.1108
0.1489
0.3968
-0.0047
0.1774
-22.762
32.1357
-9.2815
23
15.3402
16.0344
8.0158
25.4338
9.6914
12.0818
0.3609
0.3239
-0.4837
0.7097
0.4316
-0.5036
0.4426
0.4621
-0.7925
0.2736
0.1461
0.1526
0.29
0.1193
0.2035
-23.7354
18.9808
-10.3061
24
11.9597
-2.6401
5.3592
0.6012
-1.1635
2.4975
0.0548
0.0834
-0.5406
0.0238
0.0551
0.1671
0.1449
0.0568
-0.1099
0.3673
0.0281
0.1969
0.3484
0.1186
0.2374
-22.4753
8.0027
-18.316
25
5.2296
-6.5173
1.6233
8.5569
-3.3577
4.6396
-0.0294
-0.2683
0.3257
0.1256
0.1652
-0.334
-0.1946
0.4079
-0.1358
0.2404
-0.0445
0.0155
0.1876
0.0304
0.0853
-16.595
20.9896
-23.3457
26
7.0764
1.4757
-3.9915
2.5745
-3.5704
5.566
-0.8004
0.099
-0.4465
-0.0986
0.3194
-0.2855
0.3587
-0.3743
0.481
0.3765
0.0006
0.178
0.4067
0.0723
0.1883
-12.9583
18.3896
-14.2128
27
2.1737
-2.7398
0.5443
3.7147
-1.3188
2.4713
-0.2867
-0.4392
-0.1021
0.6333
0.451
0.2219
-0.2635
0.2981
-0.1642
0.546
0.0342
0.1565
0.3713
0.1416
0.1479
-20.3393
19.7338
-17.878
28
8.5191
-6.5955
-7.6872
5.4006
6.2545
8.164
0.4898
0.0729
-0.4795
-0.7261
-0.6789
0.4544
-1.3979
-0.7064
0.1891
0.756
0.5585
-0.0092
1.1296
-0.0552
0.2378
-26.8643
28.0433
-16.8377
29
3.8485
-2.3639
-0.8162
3.179
0.4218
0.1858
-0.2021
-0.0664
-0.0927
-0.0841
0.2291
0.9633
0.0642
-0.0648
-0.027
0.6071
0.0291
0.0597
0.6055
0.1491
0.5259
-44.4051
49.2658
-25.9905
30
1.4503
1.6381
1.0479
2.1495
1.4298
0.9747
0.1885
0.1415
-0.453
-0.0598
0.0471
-0.3175
-0.1286
-0.0533
-0.2355
0.5093
0.1104
-0.032
0.5729
0.1374
0.578
-48.1143
46.8799
-33.6913
31
6.0109
3.9956
-1.3684
3.2887
-4.1459
18.8848
0.4974
0.1161
0.0143
0.4608
0.2542
0.2679
0.0358
-0.5544
-0.7515
0.531
0.0697
0.2007
0.3032
0.1776
0.4456
-36.7457
40.6442
-16.1936
32
21.853
-13.7003
14.7566
9.0434
-9.3534
9.9966
-0.6917
-0.4223
1.165
0.2426
-0.1327
-0.9838
-0.4535
-0.248
0.8244
0.7168
0.0851
0.1531
0.7982
0.2094
0.7587
-53.3514
41.4115
-20.9977
33
9.2744
5.7307
-0.9506
6.4677
-1.1591
0.2202
-0.3417
0.358
-0.5071
-0.0929
0.2066
-0.2982
-0.0205
-0.0424
0.1351
0.6131
-0.0066
-0.0698
0.6685
-0.0386
0.7514
-55.1133
36.486
-26.4885
34
1.4351
-3.4709
-3.9618
9.1893
6.0765
26.5065
0.0281
0.257
-0.5637
-0.1976
-0.3537
1.6379
0.7085
-1.9084
0.3256
0.5269
-0.0555
0.0178
0.1812
-0.001
0.5158
-40.5147
36.9425
-27.1758
35
23.0347
-13.4427
0.9696
7.8737
-0.626
0.7261
-0.2476
-0.5007
0.2235
0.2074
0.3814
-0.0953
-0.0401
-0.0449
-0.1338
0.4774
0.0869
0.0698
0.4057
0.0401
0.2567
-27.8583
41.5323
-19.0768
36
4.7503
3.6427
4.9386
2.797
3.7824
5.17
0.204
-0.2808
-0.0644
0.1142
-0.1988
-0.0338
0.2488
-0.4219
-0.0052
0.623
0.0197
-0.0061
0.6863
0.0445
0.6582
-53.2858
42.9348
-33.4866
37
0.5221
0.2034
-0.0415
5.9667
-3.4121
1.9635
-0.1246
0.4574
-0.1321
-0.2846
0.1277
0.0245
0.152
0.0006
-0.0031
0.5846
0.0195
-0.0147
0.9449
-0.1125
0.7814
-60.9504
47.8606
-29.9906
38
0.0247
0.0678
0.1055
1.0747
1.6327
2.5209
0.1286
-0.0139
0.0203
0.2078
-0.5057
0.2416
0.3333
-0.8695
0.377
0.6881
0.0099
0.0985
0.7358
0.1965
0.5475
-47.0632
42.9952
-15.5362
39
0.175
-0.3468
-0.3919
1.0502
0.9869
0.9997
-0.1971
0.0841
-0.0686
0.0606
0.044
0.1184
0.2493
-0.066
0.1531
0.6028
-0.0957
0.111
0.6472
0.1269
0.5379
-45.5513
45.3029
-11.1735
40
3.9468
3.88
-0.0823
3.8185
-0.0777
0.006
-0.0259
0.0413
0.2276
-0.0079
0.0073
0.2584
0.047
-0.0096
0.0187
0.8117
0.0139
-0.1105
0.739
-0.0255
0.6173
-57.0396
53.82
-27.3663
41
10.3791
1.7874
-0.6561
20.1258
-15.9318
14.1569
-0.6589
0.2021
-0.8572
0.3895
0.4326
-0.1716
-0.3426
-0.7266
0.2263
0.4767
-0.0867
0.0327
0.5289
-0.0144
0.6252
-25.3806
-32.231
-16.8171
42
0.9474
0.3847
0.1544
2.6757
-0.2854
0.0749
0.0964
-0.1748
-0.1783
0.0588
-0.108
-0.2074
0.0308
-0.0417
0.0116
0.6646
-0.0153
0.0537
0.7413
0.0266
0.5956
-20.1333
-33.2178
-18.3882
43
12.7898
6.669
-2.5951
7.9806
-2.2008
2.4259
0.2277
-0.1552
0.5707
-0.0658
-0.1871
0.6806
0.1964
0.0811
-0.0406
0.4575
0.0429
0.0021
0.5841
-0.0571
0.5719
-15.3
-20.2092
-22.9724
44
0.7202
-1.7822
-1.6691
4.4218
4.1329
3.8714
-0.1668
-0.1184
0.0613
0.4704
0.3036
-0.2229
0.4074
0.3175
-0.1367
0.8047
-0.0189
0.0046
0.7671
0.0758
0.8243
-7.9143
-10.9325
-36.093
45
1.5646
0.1844
-3.2775
7.1988
-4.1877
15.355
-0.2922
-0.1794
-0.4265
-0.1241
-0.4519
-0.3008
0.3227
0.3346
0.7442
0.4093
0.019
-0.0115
0.562
-0.0425
0.5863
-15.8101
-24.0008
-23.5478
46
1.6656
1.8385
-0.6934
3.6278
0.1883
0.9005
0.0863
-0.9199
-0.6973
0.3121
-0.5993
-0.5546
0.2517
0.6028
0.5129
0.7266
0.0426
0.153
0.8064
0.1462
0.8435
-16.2878
-20.0802
-9.6562
47
10.9306
2.5834
0.4389
3.3467
3.9971
5.6919
-0.5826
0.9167
-1.4715
-0.008
-0.0526
-0.0233
0.4083
-0.1974
0.6352
0.929
0.2862
0.1959
0.4288
0.1375
0.7042
-8.4791
-11.7309
-24.1859
48
6.8335
3.5269
3.9475
9.446
-5.7111
10.154
0.1545
0.3624
-0.9477
-0.1004
-0.0194
-0.8868
0.2609
0.415
-0.135
0.503
-0.0611
0.0686
0.6115
-0.1369
0.6773
-27.3041
-25.2531
-16.4889
49
0.6952
-0.3071
-1.3858
1.9073
-1.468
5.2722
0.1427
-0.0219
-0.1543
-0.1998
0.0058
0.3263
-0.0939
-0.0113
-0.1485
0.3866
0.134
-0.1092
0.2224
0.1145
0.4274
-13.1229
-1.4364
-23.3098
50
0.4317
3.4192
0.6389
27.7255
5.1496
0.9586
-0.1139
0.0881
-0.1522
-0.753
0.2824
-0.873
-0.1387
0.0875
-0.1685
0.6559
0.1208
0.0242
0.6366
0.0048
0.5677
4.828
-10.8098
-23.4034
51
1.69
0.3491
0.3662
8.3602
-2.113
4.9018
0.1681
-0.2062
-0.6479
-0.0318
0.0011
-0.5929
0.2627
0.4884
-0.1691
0.5153
0.1058
-0.0043
0.3852
0.1386
0.3171
-6.2539
-3.6737
-20.5461
52
3.731
0.9958
5.0338
4.2394
-2.0571
9.738
0.3878
0.3336
-0.3662
-0.062
-0.0326
-0.2268
0.5796
0.4496
-0.3552
0.6339
0.0325
0.0064
0.6127
0.055
0.4539
-1.4939
-12.917
-9.741
53
5.5281
-5.6172
0.428
5.7876
-0.2646
0.4311
0.0501
0.2063
0.2892
0.006
-0.043
-0.3678
0.1592
0.4895
-0.0072
0.5441
0.1659
0.0178
0.6908
0.2478
0.6069
-2.9686
-2.8986
-11.4997
54
2.517
4.5706
-1.3935
10.9948
-4.7647
2.8577
-0.1968
0.2547
0.3102
-0.3787
-0.0921
-0.2093
-0.1614
0.2115
0.2889
0.646
0.188
0.0016
0.5255
0.0948
0.5922
7.0937
-11.8813
1.0597
55
5.1672
-0.6765
1.9686
1.1643
-1.9336
7.1232
0.3087
0.0499
-0.5657
-0.1495
-0.7178
-0.3393
0.672
-0.0204
0.409
0.5873
0.0018
-0.0347
0.7953
0.2113
0.4221
4.0425
-21.3318
4.3036
56
0.1046
0.8895
-0.8434
7.5974
-7.1928
6.822
-0.0945
-0.0056
-0.0046
-0.9413
0.0233
-0.0522
0.8118
-0.0692
0.0712
0.8297
-0.0329
0.0265
0.8689
-0.0201
0.8371
-5.0763
-33.4702
-8.2076
57
1.6173
1.9476
0.2528
9.6966
-0.0575
3.8628
0.1541
0.168
-0.0687
-0.1952
-0.3
0.5384
-0.0317
-0.2512
0.1459
0.3537
0.0396
-0.0826
0.4025
0.0043
0.389
-2.8595
-19.3571
1.6767
58
7.7978
-3.1802
-7.9461
4.2906
7.7107
32.1607
-0.3916
-0.428
0.7679
1.0546
0.3739
-0.8042
0.413
0.7441
0.0177
0.8653
0.1199
-0.2025
0.8724
-0.07
0.8526
-8.9631
-19.2998
-3.6516
59
2.7071
2.3812
0.3725
10.7652
8.6053
8.2487
0.1676
0.6167
-0.4343
0.3552
0.0374
-0.3128
0.5611
-0.4863
-0.205
0.5899
0.0755
-0.0626
0.5339
0.0415
0.4905
-7.3249
-22.569
1.2487
60
2.5947
5.4291
0.2842
19.8039
-1.5625
0.5856
0.3202
-0.2481
0.2931
1.3262
-0.4768
0.2104
-0.1298
-0.0373
0.1566
0.4316
0.0719
-0.1701
0.4104
0.0509
0.3438
1.9315
-20.7552
13.8267
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
H
1 - 5
2
X-RAY DIFFRACTION
2
H
6 - 16
3
X-RAY DIFFRACTION
3
H
17 - 24
4
X-RAY DIFFRACTION
4
H
25 - 39
5
X-RAY DIFFRACTION
5
H
40 - 49
6
X-RAY DIFFRACTION
6
H
50 - 59
7
X-RAY DIFFRACTION
7
H
60 - 67
8
X-RAY DIFFRACTION
8
H
68 - 81
9
X-RAY DIFFRACTION
9
H
82 - 106
10
X-RAY DIFFRACTION
10
H
107 - 128
11
X-RAY DIFFRACTION
11
H
129 - 135
12
X-RAY DIFFRACTION
12
H
141 - 146
13
X-RAY DIFFRACTION
13
H
147 - 152
14
X-RAY DIFFRACTION
14
H
153 - 161
15
X-RAY DIFFRACTION
15
H
162 - 176
16
X-RAY DIFFRACTION
16
H
177 - 186
17
X-RAY DIFFRACTION
17
H
187 - 195
18
X-RAY DIFFRACTION
18
H
196 - 204
19
X-RAY DIFFRACTION
19
H
205 - 214
20
X-RAY DIFFRACTION
20
H
215 - 223
21
X-RAY DIFFRACTION
21
L
1 - 10
22
X-RAY DIFFRACTION
22
L
11 - 17
23
X-RAY DIFFRACTION
23
L
18 - 24
24
X-RAY DIFFRACTION
24
L
25 - 35
25
X-RAY DIFFRACTION
25
L
36 - 53
26
X-RAY DIFFRACTION
26
L
54 - 69
27
X-RAY DIFFRACTION
27
L
70 - 96
28
X-RAY DIFFRACTION
28
L
97 - 108
29
X-RAY DIFFRACTION
29
L
109 - 125
30
X-RAY DIFFRACTION
30
L
126 - 135
31
X-RAY DIFFRACTION
31
L
136 - 144
32
X-RAY DIFFRACTION
32
L
145 - 152
33
X-RAY DIFFRACTION
33
L
153 - 159
34
X-RAY DIFFRACTION
34
L
160 - 164
35
X-RAY DIFFRACTION
35
L
165 - 174
36
X-RAY DIFFRACTION
36
L
175 - 186
37
X-RAY DIFFRACTION
37
L
187 - 192
38
X-RAY DIFFRACTION
38
L
193 - 198
39
X-RAY DIFFRACTION
39
L
199 - 207
40
X-RAY DIFFRACTION
40
L
208 - 212
41
X-RAY DIFFRACTION
41
U
1 - 5
42
X-RAY DIFFRACTION
42
U
6 - 23
43
X-RAY DIFFRACTION
43
U
24 - 31
44
X-RAY DIFFRACTION
44
U
32 - 36
45
X-RAY DIFFRACTION
45
U
37 - 47
46
X-RAY DIFFRACTION
46
U
48 - 53
47
X-RAY DIFFRACTION
47
U
54 - 69
48
X-RAY DIFFRACTION
48
U
70 - 79
49
X-RAY DIFFRACTION
49
U
80 - 99
50
X-RAY DIFFRACTION
50
U
100 - 105
51
X-RAY DIFFRACTION
51
U
106 - 124
52
X-RAY DIFFRACTION
52
U
125 - 164
53
X-RAY DIFFRACTION
53
U
165 - 181
54
X-RAY DIFFRACTION
54
U
182 - 199
55
X-RAY DIFFRACTION
55
U
200 - 228
56
X-RAY DIFFRACTION
56
U
229 - 234
57
X-RAY DIFFRACTION
57
U
235 - 248
58
X-RAY DIFFRACTION
58
U
249 - 255
59
X-RAY DIFFRACTION
59
U
256 - 267
60
X-RAY DIFFRACTION
60
U
268 - 277
+
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