Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0332 Å / Relative weight: 1
Reflection
Resolution: 2.3→50 Å / Num. obs: 28832 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.085 / Net I/σ(I): 16.6849
Reflection shell
Resolution: 2.3→2.38 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.3 / Rsym value: 0.979 / % possible all: 91.6
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SOLVE
phasing
REFMAC
5.5.0044
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.31→48.11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 14.965 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26413
1473
5.1 %
RANDOM
Rwork
0.21299
-
-
-
obs
0.21559
27330
99.53 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 32.675 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.64 Å2
0 Å2
-0.51 Å2
2-
-
-1.19 Å2
0 Å2
3-
-
-
1.79 Å2
Refinement step
Cycle: LAST / Resolution: 2.31→48.11 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3438
0
21
91
3550
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
3541
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.154
1.978
4808
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.646
5
440
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.697
25.232
151
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.684
15
553
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
24.841
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
541
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
2677
X-RAY DIFFRACTION
r_gen_planes_other
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
0.411
1.5
2242
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.792
2
3602
X-RAY DIFFRACTION
r_scbond_it
1.364
3
1299
X-RAY DIFFRACTION
r_scangle_it
2.116
4.5
1206
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.309→2.369 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.336
103
-
Rwork
0.292
1908
-
obs
-
-
95.13 %
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
7.0691
-0.7358
0.1835
8.7927
2.4146
7.924
-0.1545
-1.0454
0.1481
1.024
-0.0361
0.182
0.6037
-0.8256
0.1906
0.1949
-0.0119
0.0132
0.2729
-0.0209
0.1698
32.9509
14.1056
108.3979
2
4.185
-0.0664
0.5027
3.2725
-1.0963
9.5483
0.1067
-0.8393
-0.0147
0.5277
-0.0543
-0.215
-0.1756
0.5637
-0.0524
0.2419
-0.0352
-0.0389
0.2661
-0.0279
0.2844
43.3521
16.0731
108.0479
3
3.4554
2.6686
2.1509
3.7043
1.564
1.3481
-0.3119
-0.1836
0.3956
-0.2485
0.0373
-0.1477
-0.2185
-0.1273
0.2746
0.1804
-0.0284
-0.0031
0.2042
0.0423
0.3099
45.9939
21.1345
87.6727
4
6.1225
-3.3832
-3.3377
5.9416
1.4551
11.528
-0.2246
0.7828
-0.1332
-1.0847
-0.0502
-0.3826
0.1234
1.1631
0.2748
0.3738
-0.1525
0.1225
0.444
0.0082
0.3235
45.5307
18.1689
74.1829
5
1.9816
-0.6104
-0.4393
1.8561
-0.0598
1.8439
-0.0461
0.1447
0.0373
-0.2174
0.0074
-0.1333
-0.0008
-0.0248
0.0387
0.1591
-0.0221
0.008
0.2076
0.0113
0.2318
41.233
9.5627
92.9594
6
4.5936
1.0697
0.7756
4.4925
-0.1889
0.8156
-0.1461
0.352
-0.0665
-0.3198
0.0267
-0.2798
0.0425
0.0772
0.1194
0.2211
-0.0013
0.0032
0.2183
0.0014
0.1967
40.1013
9.873
89.8847
7
2.5174
0.612
0.9352
3.8334
-1.2196
2.3176
0.011
0.1149
-0.2239
-0.3721
0.0091
-0.3278
0.2381
0.2188
-0.0201
0.163
-0.0087
0.0428
0.2209
0.0044
0.2084
42.1119
5.8969
86.7175
8
2.0062
1.9835
-0.108
3.2549
0.8113
1.1704
0.0304
0.061
-0.0481
0.0222
-0.0546
-0.1884
0.0192
0.0674
0.0242
0.1345
0.0454
-0.0101
0.2112
0.021
0.2925
43.7914
-1.6329
96.097
9
2.4122
1.8418
0.6555
4.6399
0.7146
2.8041
-0.0613
0.159
-0.1698
-0.2226
-0.0256
-0.2711
0.189
-0.0046
0.0869
0.1101
0.0487
0.0648
0.1935
-0.0272
0.2926
43.7172
-14.7102
92.0284
10
4.6923
1.578
1.3236
5.7001
-2.7653
7.4989
-0.1599
-0.2696
0.236
0.2297
0.1992
0.0218
-0.0511
-0.4565
-0.0394
0.1978
-0.0125
0.0346
0.1887
-0.0091
0.2453
32.0416
-12.2172
97.7869
11
4.1348
-1.3375
1.6839
9.2944
-3.4356
1.8577
-0.1201
0.4311
0.3611
-0.3361
0.0442
0.1211
-0.0514
-0.1565
0.0759
0.2614
0.0326
0.0312
0.4246
0.0062
0.2564
27.2504
-12.1749
85.9291
12
2.2423
-0.7132
2.3844
2.6396
-2.9249
8.727
-0.1089
0.1296
-0.1593
0.0165
0.0919
-0.0852
0.3292
0.0902
0.017
0.1688
-0.0197
0.0171
0.2113
-0.0114
0.2351
30.2092
-21.5261
99.1104
13
3.9467
-3.5355
-3.8618
11.9852
1.1423
8.1535
-0.0808
0.0037
-0.6055
-0.4231
-0.2473
-0.5685
0.6344
0.6642
0.3281
0.2586
0.0185
0.0019
0.3006
-0.0411
0.3673
36.1876
-25.3605
103.5648
14
5.7753
-4.5068
-4.0197
4.1386
1.4476
7.5056
-0.205
0.7164
-0.7293
0.0758
-0.4383
0.4552
0.543
-0.9095
0.6433
0.5758
-0.0571
-0.2028
0.1546
-0.0405
0.3424
21.2681
7.1494
41.5556
15
12.3046
-7.8753
-1.1401
6.4016
0.1308
0.3961
0.4075
0.4149
-0.6193
0.832
-0.2544
1.0986
-0.6007
-0.0578
-0.1532
1.1971
-0.0065
0.2368
0.2508
-0.0043
0.6743
12.002
19.7984
41.567
16
4.7103
1.0307
-2.0645
4.6504
0.452
2.8393
0.3201
0.3249
0.2569
0.0505
0.0231
0.6668
-0.7421
-0.1033
-0.3432
0.5898
0.1451
0.0105
0.1516
0.0061
0.2411
17.8758
38.414
51.4452
17
1.015
0.6832
-2.1283
6.6919
-0.1359
4.9864
-0.1646
0.0715
-0.0081
-0.5559
0.2093
-0.2238
-0.0225
-0.3132
-0.0448
0.4934
0.0725
-0.0688
0.2109
0.035
0.0449
21.2378
20.3182
50.6407
18
4.2486
-0.5492
0.3265
4.7083
2.2009
5.2181
0.041
0.1276
0.0565
-0.0481
-0.11
0.8468
-0.6953
-0.6442
0.0691
0.4932
0.1072
-0.0802
0.1205
0.0439
0.2355
14.7522
33.8661
53.8113
19
1.2447
1.5878
0.6558
8.8241
-2.4254
2.051
0.0846
-0.2537
-0.0679
0.4187
0.2451
0.5968
-0.3493
-0.4224
-0.3297
0.5178
0.1117
-0.0712
0.1699
0.027
0.103
19.3338
29.0277
60.9658
20
1.4046
0.0378
0.5679
8.345
-5.6799
6.0256
0.0447
-0.0886
0.0878
-0.3864
0.3718
0.8225
0.1033
-1.0594
-0.4166
0.3328
-0.01
-0.1813
0.3444
0.0163
0.1545
10.8067
18.7093
56.5103
21
4.7459
1.7272
0.6645
2.208
-1.0442
9.8671
-0.0266
-0.1136
0.0764
-0.2268
-0.1378
0.3695
-0.1046
-0.315
0.1644
0.2385
0.0283
-0.0104
0.2465
0.0044
0.2265
19.7704
18.9601
69.4394
22
4.305
0.7685
-0.3059
0.9502
-0.8542
4.6672
0.0236
0.1355
0.301
0.0747
-0.0195
0.3833
-0.6168
-0.4167
-0.004
0.192
0.0796
-0.0047
0.2777
-0.0014
0.1956
18.2426
20.3156
79.1862
23
0.9101
-1.2447
-2.7558
1.735
3.8707
8.664
0.3737
0.5852
-0.2213
-0.3396
-0.8672
0.2178
-0.7104
-2.2677
0.4934
0.1669
-0.0438
-0.1962
1.156
0.2694
0.2756
9.4914
14.5781
69.885
24
5.3322
1.3616
1.6019
6.0618
-0.1957
6.7923
0.1358
0.3328
-0.0058
-0.3541
-0.0813
-0.3699
0.3384
0.1902
-0.0545
0.2557
0.0493
0.0026
0.2556
0.0735
0.1025
26.2564
13.2835
70.2494
25
8.3536
-1.1931
1.3399
5.7538
-1.7764
3.6248
-0.4636
0.2676
0.2396
-0.4555
0.4912
-0.2021
-0.492
-0.2994
-0.0276
0.2169
-0.0384
-0.0026
0.265
0.007
0.145
30.2139
16.78
79.4043
26
6.614
1.1383
-2.5765
6.0076
-2.563
1.7779
-0.044
1.0246
0.1108
-0.7963
0.0671
-0.0317
0.3161
-0.3454
-0.023
0.2431
0.0677
0.0413
0.3215
0.0157
0.3367
32.9672
4.9619
74.7169
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
350 - 359
2
X-RAY DIFFRACTION
2
A
360 - 369
3
X-RAY DIFFRACTION
3
A
370 - 378
4
X-RAY DIFFRACTION
4
A
379 - 390
5
X-RAY DIFFRACTION
5
A
401 - 427
6
X-RAY DIFFRACTION
6
A
428 - 447
7
X-RAY DIFFRACTION
7
A
451 - 488
8
X-RAY DIFFRACTION
8
A
489 - 515
9
X-RAY DIFFRACTION
9
A
516 - 549
10
X-RAY DIFFRACTION
10
A
550 - 563
11
X-RAY DIFFRACTION
11
A
564 - 581
12
X-RAY DIFFRACTION
12
A
582 - 592
13
X-RAY DIFFRACTION
13
A
593 - 599
14
X-RAY DIFFRACTION
14
B
342 - 360
15
X-RAY DIFFRACTION
15
B
361 - 372
16
X-RAY DIFFRACTION
16
B
373 - 408
17
X-RAY DIFFRACTION
17
B
409 - 435
18
X-RAY DIFFRACTION
18
B
436 - 463
19
X-RAY DIFFRACTION
19
B
464 - 488
20
X-RAY DIFFRACTION
20
B
489 - 505
21
X-RAY DIFFRACTION
21
B
506 - 514
22
X-RAY DIFFRACTION
22
B
515 - 536
23
X-RAY DIFFRACTION
23
B
537 - 548
24
X-RAY DIFFRACTION
24
B
549 - 568
25
X-RAY DIFFRACTION
25
B
569 - 587
26
X-RAY DIFFRACTION
26
B
588 - 597
+
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