Resolution: 1.9→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 95.3
-
Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
HKL-3000
phasing
REFMAC
5.5.0109
refinement
HKL-3000
datareduction
HKL-3000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.586 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22531
3593
5.1 %
RANDOM
Rwork
0.17438
-
-
-
all
0.18
71044
-
-
obs
0.17695
67451
97.61 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 25.867 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.61 Å2
0 Å2
-1.66 Å2
2-
-
1.71 Å2
0 Å2
3-
-
-
-1.75 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→40 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7312
0
2
681
7995
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.022
7439
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
4851
X-RAY DIFFRACTION
r_angle_refined_deg
1.69
1.974
10090
X-RAY DIFFRACTION
r_angle_other_deg
1.357
3
12038
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.568
5
982
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.616
26.224
286
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.165
15
1306
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.825
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.109
0.2
1199
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
8285
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1283
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.219
1.5
4865
X-RAY DIFFRACTION
r_mcbond_other
0.27
1.5
1999
X-RAY DIFFRACTION
r_mcangle_it
2.161
2
7854
X-RAY DIFFRACTION
r_scbond_it
3.543
3
2574
X-RAY DIFFRACTION
r_scangle_it
5.547
4.5
2233
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.901→1.951 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.309
258
-
Rwork
0.256
4668
-
obs
-
-
91.51 %
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
0.6401
-0.3603
0.5428
1.7803
-0.3228
0.9646
0.0906
-0.1292
0.0211
0.1259
-0.0467
-0.0982
0.067
-0.0332
-0.0439
0.1688
-0.0224
-0.0014
0.1767
0.0217
0.1606
24.8074
17.09
37.7235
2
3.9747
-3.7193
0.8288
5.4841
-0.6791
1.4769
-0.0388
-0.4006
-0.0117
0.1039
0.0176
0.1024
0.1896
-0.3629
0.0213
0.1441
-0.057
0.0026
0.1817
0.0297
0.171
10.5828
16.875
35.2063
3
1.2036
-0.7697
0.9182
2.6952
-0.872
0.8929
-0.015
-0.075
0.1432
-0.054
0.0306
0.2676
0.0483
-0.185
-0.0156
0.1308
-0.0089
0.0124
0.2023
0.0002
0.1933
13.7216
29.4521
32.5126
4
1.9367
-3.7164
5.3255
8.4184
-9.1189
15.6038
-0.2084
-0.1126
0.0356
0.5497
0.2338
-0.2675
-0.4049
-0.2788
-0.0254
0.0989
-0.05
0.0836
0.2638
-0.1148
0.2466
10.5198
28.4366
37.8675
5
1.2165
1.351
-0.3671
2.8047
-1.7301
2.1685
-0.0534
0.0293
0.0526
0.02
0.1133
0.0831
0.05
-0.3102
-0.0599
0.1355
0.0114
-0.0007
0.1718
-0.0029
0.16
18.3231
29.5589
31.2766
6
5.4637
1.441
-3.1349
8.7736
-0.526
6.5083
-0.0642
0.0547
0.4224
-0.1846
-0.0243
0.2488
-0.0594
-0.1963
0.0885
0.1387
0.0079
-0.0033
0.146
0.0064
0.1566
20.217
38.7093
31.9184
7
1.026
0.7405
0.1394
1.1547
-0.1603
1.2847
0.0259
-0.0646
0.0586
0.0966
-0.0483
0.0829
-0.0909
-0.0876
0.0224
0.1546
0.0031
0.0045
0.1467
0.0028
0.1464
25.7168
34.3834
35.6125
8
1.323
0.2035
-0.3221
0.9406
0.0861
1.3207
-0.0353
0.0561
-0.0585
-0.0595
0.0249
-0.0649
0.0258
0.1239
0.0104
0.146
-0.0005
-0.0006
0.1426
-0.0002
0.162
34.5886
28.4998
24.9843
9
1.4569
-0.2224
0.1888
1.1583
0.2214
1.2345
-0.0051
0.1743
0.0021
-0.1693
0.0034
-0.0418
0.0485
0.0994
0.0017
0.1624
-0.0113
0.0105
0.1657
0.0014
0.1443
37.408
34.5386
20.1691
10
1.3623
0.8836
1.1025
1.6044
0.9803
3.2879
-0.0106
0.1249
-0.029
-0.0504
0.0364
-0.0115
0.0977
0.0445
-0.0258
0.1485
0.0148
0.0082
0.1535
0.0145
0.1596
34.2029
27.9611
28.0315
11
2.2103
0.3877
0.3634
1.3736
0.8213
2.6069
-0.0218
0.1521
-0.2112
-0.0269
0.1048
-0.1016
0.1417
0.1866
-0.083
0.1579
0.0173
0.0064
0.1237
-0.0024
0.1726
37.588
19.0704
25.7692
12
2.278
-0.1563
0.5303
0.9378
-0.5918
0.9149
0.0087
0.1201
-0.262
-0.0451
0.06
-0.1188
0.1794
-0.0137
-0.0686
0.2008
0.0044
-0.0087
0.1417
-0.0289
0.1903
28.5433
10.8644
23.8478
13
4.2869
0.3014
1.6301
0.9975
0.2154
0.8519
-0.0163
0.0248
0.0909
-0.0233
-0.0394
-0.0472
0.1047
-0.0482
0.0557
0.1805
-0.0071
0.0103
0.1448
0.015
0.1416
26.6384
16.5235
28.2954
14
4.9662
-2.2605
2.7304
3.128
-1.7918
3.2667
-0.039
0.0801
-0.1513
-0.1972
0.1589
0.15
0.1552
-0.2071
-0.1198
0.1864
-0.054
-0.012
0.1628
0.0283
0.1633
12.6303
12.149
26.6888
15
2.3255
-0.0899
1.1324
2.886
-0.9964
6.0231
-0.1516
0.0841
-0.3368
-0.1547
-0.0854
-0.2992
0.3731
-0.1254
0.237
0.1883
0.0037
-0.0183
0.1475
0.0145
0.2268
26.9263
4.2585
33.3316
16
2.6897
0.7954
-1.8077
1.7637
-2.3851
3.4648
0.1632
0.1091
0.1774
0.1076
0.1478
0.2386
-0.1704
-0.1875
-0.311
0.1944
0.0104
0.0266
0.138
0.026
0.2492
35.5362
65.1766
31.9422
17
1.4849
0.214
1.0713
0.7819
-0.3502
2.8802
0.0137
-0.0189
0.1605
0.0429
-0.0214
0.0317
-0.0975
-0.0122
0.0077
0.1568
-0.0221
-0.0036
0.1503
0.0141
0.1861
44.816
64.905
35.258
18
0.6037
0.2039
0.2481
1.1706
-1.0749
1.5386
0.0002
0.0136
0.078
0.1714
0.0184
0.0691
-0.1606
0.0398
-0.0186
0.1813
-0.0109
-0.0028
0.1657
-0.0045
0.1618
45.5453
61.03
41.2357
19
1.893
0.2611
-0.5172
10.9679
-2.4257
0.663
0.0081
-0.283
0.0862
0.4421
0.0754
0.231
-0.1094
-0.0058
-0.0836
0.2132
0.0276
0.026
0.2951
-0.0104
0.1276
40.3418
54.5942
50.9536
20
2.1942
-1.1249
0.5393
4.1352
0.3923
1.4726
-0.0201
-0.1031
0.0778
0.0942
-0.0067
0.0702
-0.104
-0.0617
0.0268
0.164
-0.0253
0.0066
0.1733
0.023
0.1517
42.526
57.9101
42.0135
21
4.8992
-2.3126
-1.2452
2.8302
0.6259
1.7399
-0.0266
-0.1605
-0.1087
0.144
0.0583
-0.1209
0.1413
0.0855
-0.0317
0.1614
-0.0051
-0.0115
0.1448
0.0042
0.1506
42.0899
43.6472
41.3316
22
0.6997
0.3386
0.2221
1.1173
0.0932
0.3558
-0.0019
-0.0819
0.0147
0.0893
-0.0124
0.0865
-0.0197
-0.0167
0.0143
0.1464
-0.0017
0.0031
0.1398
0.0051
0.1469
35.8023
49.0983
37.4732
23
0.9518
0.1058
0.069
0.5936
-0.0097
0.7116
-0.0192
0.0698
-0.0304
-0.0209
0.0265
-0.0148
-0.0063
0.0529
-0.0073
0.1431
-0.0157
-0.0071
0.1603
0.0075
0.145
43.0156
45.1083
26.5278
24
9.6399
-1.9565
0.4412
8.4818
2.6601
0.9792
0.0854
0.0333
-0.2375
0.2644
0.0789
-0.3815
0.147
0.1073
-0.1643
0.1878
0.1084
-0.0013
0.2654
-0.0264
0.1928
49.9664
33.6829
27.9053
25
2.3692
-0.3097
-0.1239
0.8098
0.638
1.6474
-0.0616
0.102
0.0525
-0.0547
0.0315
-0.0389
-0.0864
0.1398
0.0301
0.1639
-0.0063
-0.0008
0.1555
0.0222
0.1292
41.5964
46.5053
22.6505
26
14.2722
7.5798
3.3907
14.3112
7.625
4.112
0.0472
-0.2072
-0.006
-0.1484
0.2751
-0.5602
-0.0549
0.1147
-0.3223
0.1397
-0.1642
0.0195
0.4691
0.1273
0.125
55.1532
51.8066
16.0109
27
1.7057
1.0152
-0.0777
1.6269
0.1568
1.3973
-0.0906
0.0727
0.025
-0.0576
0.0594
0.044
-0.0775
0.0299
0.0312
0.1545
-0.0022
-0.0061
0.1567
0.0229
0.1372
44.5885
55.4313
20.76
28
1.2098
0.4594
0.7964
0.7784
0.1132
1.7635
-0.0459
0.0653
0.1198
-0.047
0.0372
0.0032
-0.0491
0.0709
0.0087
0.159
-0.0177
-0.0101
0.1524
0.0176
0.1616
48.8785
61.304
23.9328
29
1.4617
-0.4368
1.8973
1.0657
-1.3263
5.0983
-0.0312
0.0264
0.1906
0.0667
0.0168
-0.1175
-0.1044
0.3208
0.0144
0.1729
-0.0515
-0.019
0.1798
0.0136
0.1895
54.6163
67.939
35.3076
30
2.3687
3.7232
2.4888
5.8712
3.496
12.1503
-0.153
0.0932
0.04
-0.2251
0.1598
0.0588
-0.4188
-0.0055
-0.0068
0.1913
-0.0269
-0.0469
0.161
0.0425
0.2152
45.988
72.9328
20.5259
31
1.3128
0.5897
-0.2089
0.8632
0.0629
1.2039
-0.0526
0.1636
0.0995
-0.1776
0.0489
0.059
-0.0185
-0.051
0.0037
0.1855
-0.0165
-0.0094
0.1393
0.0022
0.1669
20.4337
64.8479
-3.4357
32
1.0105
0.3883
-0.5547
1.3596
0.3312
3.5175
-0.0511
-0.0048
0.219
-0.097
-0.0171
0.0577
-0.2226
-0.0934
0.0682
0.1712
-0.0025
-0.0174
0.1328
-0.007
0.1542
21.2412
72.1658
9.0751
33
0.9872
0.3086
0.232
1.467
-1.0431
2.5991
0.061
-0.11
-0.0183
0.1507
-0.1498
-0.066
-0.0508
0.0556
0.0888
0.1721
-0.0094
-0.0036
0.1446
-0.0266
0.1529
17.3871
60.2195
12.286
34
3.8976
5.765
0.8642
14.3177
-1.4801
1.5074
-0.0662
-0.2685
0.1126
0.1675
0.1134
0.2899
-0.1312
-0.3105
-0.0473
0.1595
-0.012
0.0219
0.1785
-0.0226
0.1693
10.528
63.3198
15.4495
35
0.6385
0.1966
0.6215
3.2653
-0.7363
1.7793
-0.0083
-0.0915
0.1161
0.0003
-0.0747
0.0836
-0.0703
-0.0731
0.083
0.1562
-0.0248
-0.003
0.1569
-0.0119
0.1572
16.1318
62.7408
8.7509
36
5.5256
-2.9883
1.1079
3.6663
-1.0366
1.8058
0.0114
-0.2726
-0.003
0.1029
0.0225
0.0324
0.0559
-0.1459
-0.0339
0.161
-0.0228
0.0023
0.1506
0.0006
0.1301
13.6011
49.8126
11.9217
37
0.9054
0.4445
0.5584
1.6835
-0.2001
0.66
0.0189
-0.04
0.0126
0.0055
-0.0062
0.0124
-0.0029
0.0033
-0.0127
0.1532
-0.0081
0.0055
0.1484
0.0002
0.137
14.1358
51.0206
3.5218
38
2.3358
-0.3257
-0.23
1.2871
0.31
0.6101
0.0254
0.0619
-0.1039
-0.0957
0.0283
-0.0732
0.0613
0.0509
-0.0537
0.1798
-0.0131
-0.0003
0.1629
-0.0096
0.1462
21.9032
47.2482
-1.1658
39
0.8606
0.0705
0.442
0.8737
-0.4489
1.5084
0.0826
0.0291
-0.162
-0.0238
-0.0089
-0.2516
0.0898
0.1577
-0.0736
0.1572
-0.0002
-0.0202
0.1558
-0.0173
0.2096
25.4533
38.3165
1.4737
40
3.8544
0.6509
2.0404
2.0009
0.5992
1.1217
0.0036
0.0818
-0.0125
-0.001
0.015
-0.1256
0.0223
0.0739
-0.0186
0.1665
0.0102
0.0236
0.1843
0.0034
0.125
20.9786
47.3074
-3.0583
41
3.2313
3.5457
-4.333
7.2566
-0.8779
10.2864
0.0976
0.0022
-0.2024
-0.0181
0.0167
-0.5497
-0.2857
-0.0304
-0.1143
0.1061
0.0287
-0.0328
0.1995
-0.0379
0.2861
37.9231
51.8386
0.5047
42
2.0274
-0.478
0.417
2.4006
0.8374
2.4377
0.0334
0.2045
-0.099
-0.2062
-0.0044
-0.2028
-0.0288
0.1323
-0.0291
0.1855
-0.028
0.0374
0.1578
0.0051
0.1636
28.4837
50.8858
-8.9275
43
0.7689
0.3512
-0.738
2.5038
-0.6085
3.0037
-0.1014
-0.0449
0.0269
-0.0828
0.0991
-0.3983
-0.052
0.1649
0.0023
0.1478
-0.0429
0.0363
0.1801
0.008
0.21
36.6387
62.0208
-1.4009
44
0.9432
0.4392
0.4556
1.4395
1.0557
2.5197
-0.0336
0.0176
0.0002
-0.064
0.0214
-0.203
-0.0402
0.0531
0.0122
0.1592
-0.0065
0.0082
0.1424
0.026
0.1835
30.039
61.2467
0.5293
45
1.0658
-0.2336
-0.2883
0.9214
0.0387
6.6393
-0.0155
0.0247
0.1411
-0.1468
0.0551
-0.1408
-0.2002
0.2152
-0.0396
0.188
-0.0461
-0.0086
0.1414
0.018
0.1897
31.0319
71.1336
-0.432
46
2.299
-0.6327
1.1366
1.3101
0.1726
0.7913
0.2471
-0.2361
-0.2155
0.1911
-0.1407
-0.0284
0.1908
-0.2139
-0.1064
0.2435
-0.1307
-0.0881
0.1543
0.053
0.1908
-3.3134
20.0498
4.1173
47
1.1265
0.1798
1.0335
4.0525
-1.9367
2.06
0.248
-0.1959
-0.1687
0.1224
-0.0655
0.0125
0.1525
-0.1867
-0.1824
0.1896
-0.0569
-0.0569
0.2146
-0.0102
0.1913
-5.4834
24.2607
-2.831
48
4.6952
8.1979
-2.9509
14.4447
-4.6771
3.9484
0.0808
-0.0417
0.2194
0.131
-0.2415
0.4188
-0.0729
-0.4518
0.1607
0.1372
-0.0067
-0.0229
0.2689
0.0152
0.2046
-10.853
35.5307
-5.3166
49
3.7859
2.7544
-0.5289
2.7619
-0.2462
0.4977
0.1335
0.1233
-0.0968
0.14
0.0097
-0.0778
0.1284
-0.1517
-0.1432
0.2392
-0.0679
-0.0396
0.1783
-0.0237
0.1473
-2.6429
29.7656
-3.8109
50
7.809
-0.5751
-2.5192
4.3601
0.0142
4.6424
-0.0579
0.2558
0.2232
-0.2149
-0.0524
0.086
-0.2117
-0.1516
0.1103
0.1719
-0.0107
-0.0068
0.1539
-0.0019
0.131
0.489
39.1166
-4.6976
51
1.2428
1.1461
0.0819
1.0758
0.1798
1.8021
0.0682
-0.0246
0.0424
0.0136
-0.0247
0.0445
-0.0136
-0.1438
-0.0435
0.1798
-0.0122
-0.0194
0.1407
0.008
0.1423
3.3019
36.1871
1.7019
52
3.4001
-1.4778
-0.8234
1.9527
0.6828
0.416
0.1053
-0.0706
0.0647
0.0906
0.0818
-0.2685
0.1843
-0.0012
-0.1871
0.277
-0.0206
-0.1361
0.1108
-0.0109
0.1807
13.6235
28.2446
1.3105
53
1.4374
0.7345
-0.5352
1.9458
0.5938
2.179
-0.0002
0.3088
-0.3288
-0.3838
0.2421
0.0248
0.1059
0.2091
-0.2419
0.2112
0.044
-0.1186
0.2094
-0.1308
0.264
19.0884
34.1444
-9.6834
54
1.599
-0.3282
-0.5136
1.4599
0.6834
1.0263
0.1326
0.0452
-0.1496
-0.0263
0.0092
-0.1128
0.1193
-0.0309
-0.1419
0.1786
-0.0059
-0.0601
0.1364
0.0106
0.1834
17.3268
29.5026
2.4281
55
6.535
6.584
4.2516
12.6664
-7.734
26.7527
0.056
-0.1852
-0.2246
-0.4063
-0.2058
-0.4234
1.0817
-0.1274
0.1498
0.2842
-0.0247
-0.2307
0.1062
-0.0341
0.2971
17.3334
13.5847
-6.0483
56
2.7808
0.029
0.5253
1.4067
0.8693
2.0065
0.1951
-0.1232
-0.2082
0.2776
-0.0472
-0.1621
0.3018
0.1282
-0.1479
0.2275
-0.0357
-0.1277
0.114
0.0414
0.2179
17.1177
21.2846
5.7147
57
3.4261
2.8412
-0.7154
2.373
-0.7405
1.5571
0.1262
0.0804
-0.419
0.0765
0.0792
-0.2985
0.1048
-0.1547
-0.2054
0.2592
0.008
-0.2082
0.0169
0.0115
0.3477
10.0776
10.6704
-0.9158
58
4.6174
2.0127
2.6309
0.9246
1.3553
2.4693
0.1109
0.0801
-0.3023
0.0424
-0.0128
-0.1057
0.078
-0.1073
-0.0981
0.2527
-0.0152
-0.1488
0.1269
-0.0134
0.2069
2.6797
16.8052
-3.4102
59
1.2232
-2.6561
1.3462
11.247
3.5334
9.096
0.2005
0.1496
-0.1814
0.2431
-0.2263
0.5349
0.9441
0.2913
0.0257
0.3348
-0.1077
-0.3099
0.1078
0.1661
0.4232
-2.8764
9.1003
-0.6544
60
17.278
-31.5304
9.0698
57.5461
-16.5544
4.7628
-1.2316
-1.0021
-0.3077
1.7929
1.6357
0.5892
-0.4966
-0.5424
-0.4041
0.765
-0.2678
-0.4966
0.2113
0.2702
0.4827
4.2502
6.2814
9.6568
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
2 - 18
2
X-RAY DIFFRACTION
2
A
19 - 31
3
X-RAY DIFFRACTION
3
A
32 - 53
4
X-RAY DIFFRACTION
4
A
54 - 58
5
X-RAY DIFFRACTION
5
A
59 - 77
6
X-RAY DIFFRACTION
6
A
78 - 83
7
X-RAY DIFFRACTION
7
A
84 - 108
8
X-RAY DIFFRACTION
8
A
109 - 130
9
X-RAY DIFFRACTION
9
A
131 - 149
10
X-RAY DIFFRACTION
10
A
150 - 164
11
X-RAY DIFFRACTION
11
A
165 - 189
12
X-RAY DIFFRACTION
12
A
190 - 206
13
X-RAY DIFFRACTION
13
A
207 - 222
14
X-RAY DIFFRACTION
14
A
223 - 238
15
X-RAY DIFFRACTION
15
A
239 - 246
16
X-RAY DIFFRACTION
16
B
2 - 8
17
X-RAY DIFFRACTION
17
B
9 - 25
18
X-RAY DIFFRACTION
18
B
26 - 46
19
X-RAY DIFFRACTION
19
B
47 - 56
20
X-RAY DIFFRACTION
20
B
57 - 73
21
X-RAY DIFFRACTION
21
B
74 - 82
22
X-RAY DIFFRACTION
22
B
83 - 107
23
X-RAY DIFFRACTION
23
B
108 - 134
24
X-RAY DIFFRACTION
24
B
135 - 140
25
X-RAY DIFFRACTION
25
B
141 - 166
26
X-RAY DIFFRACTION
26
B
167 - 172
27
X-RAY DIFFRACTION
27
B
173 - 196
28
X-RAY DIFFRACTION
28
B
197 - 222
29
X-RAY DIFFRACTION
29
B
223 - 241
30
X-RAY DIFFRACTION
30
B
242 - 246
31
X-RAY DIFFRACTION
31
C
2 - 18
32
X-RAY DIFFRACTION
32
C
19 - 31
33
X-RAY DIFFRACTION
33
C
32 - 50
34
X-RAY DIFFRACTION
34
C
51 - 56
35
X-RAY DIFFRACTION
35
C
57 - 72
36
X-RAY DIFFRACTION
36
C
73 - 86
37
X-RAY DIFFRACTION
37
C
87 - 104
38
X-RAY DIFFRACTION
38
C
105 - 128
39
X-RAY DIFFRACTION
39
C
129 - 149
40
X-RAY DIFFRACTION
40
C
150 - 162
41
X-RAY DIFFRACTION
41
C
163 - 169
42
X-RAY DIFFRACTION
42
C
170 - 190
43
X-RAY DIFFRACTION
43
C
191 - 202
44
X-RAY DIFFRACTION
44
C
203 - 227
45
X-RAY DIFFRACTION
45
C
228 - 246
46
X-RAY DIFFRACTION
46
D
2 - 26
47
X-RAY DIFFRACTION
47
D
27 - 46
48
X-RAY DIFFRACTION
48
D
47 - 56
49
X-RAY DIFFRACTION
49
D
57 - 77
50
X-RAY DIFFRACTION
50
D
78 - 83
51
X-RAY DIFFRACTION
51
D
84 - 107
52
X-RAY DIFFRACTION
52
D
108 - 125
53
X-RAY DIFFRACTION
53
D
126 - 140
54
X-RAY DIFFRACTION
54
D
141 - 163
55
X-RAY DIFFRACTION
55
D
164 - 170
56
X-RAY DIFFRACTION
56
D
171 - 189
57
X-RAY DIFFRACTION
57
D
190 - 206
58
X-RAY DIFFRACTION
58
D
207 - 229
59
X-RAY DIFFRACTION
59
D
230 - 241
60
X-RAY DIFFRACTION
60
D
242 - 246
+
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