Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54178 Å / Relative weight: 1
Reflection
Resolution: 1.76→50 Å / Num. obs: 18412 / % possible obs: 98 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.085 / Χ2: 1.132 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
1.76-1.82
3.9
0.388
1739
1.339
94.8
1.82-1.9
6.7
0.414
1787
1.26
96.4
1.9-1.98
7.6
0.283
1783
1.094
97.1
1.98-2.09
7.7
0.207
1800
1.131
97.8
2.09-2.22
7.8
0.154
1827
1.11
97.9
2.22-2.39
7.8
0.134
1839
1.105
98.8
2.39-2.63
7.8
0.11
1839
1.091
98.5
2.63-3.01
7.8
0.083
1881
1.136
99.5
3.01-3.79
7.7
0.06
1902
1.106
99.6
3.79-50
7.4
0.055
2015
1.096
99.3
-
Phasing
Phasing
Method: molecular replacement
-
Processing
Software
Name
Version
Classification
NB
SCALEPACK
datascaling
AMoRE
phasing
REFMAC
refinement
PDB_EXTRACT
3.1
dataextraction
DENZO
datareduction
Refinement
Resolution: 1.76→23.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.965 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21902
937
5.1 %
RANDOM
Rwork
0.17814
-
-
-
obs
0.18026
17434
97.79 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 20.157 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.67 Å2
0 Å2
0 Å2
2-
-
0.5 Å2
0 Å2
3-
-
-
1.17 Å2
Refine analyze
Luzzati coordinate error obs: 0.215 Å
Refinement step
Cycle: LAST / Resolution: 1.76→23.25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1474
0
86
144
1704
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.022
1586
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1026
X-RAY DIFFRACTION
r_angle_refined_deg
1.294
2.029
2163
X-RAY DIFFRACTION
r_angle_other_deg
0.814
3
2532
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.083
5
198
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
42.67
25
52
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
9.621
15
247
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.11
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.076
0.2
258
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
1712
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
278
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
0.682
1.5
1002
X-RAY DIFFRACTION
r_mcbond_other
0.144
1.5
413
X-RAY DIFFRACTION
r_mcangle_it
1.225
2
1605
X-RAY DIFFRACTION
r_scbond_it
1.538
3
584
X-RAY DIFFRACTION
r_scangle_it
2.402
4.5
557
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.76→1.801 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.284
70
-
Rwork
0.251
1185
-
obs
-
-
91.41 %
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
1.9839
-1.6991
-1.0716
0.2833
-0.8751
4.0158
-0.1358
-0.126
-0.1907
0.1167
0.2019
0.0291
0.1292
-0.1614
-0.066
0.1398
0.0174
0.0218
0.0683
0.0248
0.118
20.079
18.368
28.032
2
0.4892
-1.7115
0.2418
0.78
-0.119
2.5473
-0.0438
-0.0318
0.0093
0.1262
-0.0265
-0.1033
0.0956
0.019
0.0704
0.1295
0.0188
0.0103
0.1158
0.0029
0.0875
21.163
21.422
30.258
3
8.848
-0.1666
1.2462
4.119
0.1526
-1.3189
0.1527
0.3796
-0.2535
-0.0003
-0.1382
0.1088
0.1306
-0.0397
-0.0145
0.1431
0.009
-0.017
0.0722
-0.0075
0.127
19.455
16.136
16.387
4
11.5273
1.5362
-4.3339
-0.8415
2.4115
5.9331
-0.5302
-0.3614
0.4266
0.1454
0.3529
-0.0161
-0.1349
0.0415
0.1773
0.1842
0.0742
-0.0361
0.1181
-0.0382
0.0973
20.924
32.96
28.554
5
3.4424
0.655
1.3337
2.4801
-0.0971
0.052
0.0442
-0.1268
0.0178
-0.0001
-0.0349
-0.0538
-0.0522
-0.0487
-0.0093
0.1273
0.0056
0.0096
0.0764
-0.0022
0.0936
14.704
28.519
20.089
6
7.6903
-2.0423
-1.8012
4.5956
3.4534
3.855
0.1613
0.2808
0.0752
-0.0211
-0.0871
0.223
0.1685
-0.4024
-0.0741
0.0642
-0.015
0.0058
0.1276
0.0836
0.0872
0.436
34.16
13.247
7
1.4273
1.2029
0.5765
1.834
0.3458
0.3868
0.015
0.0689
-0.0304
-0.0051
-0.0657
0.0191
0.0176
-0.005
0.0507
0.1153
0.0141
-0.0033
0.0865
0.0065
0.0972
25.7
26.427
17.738
8
4.8338
0.4999
0.9841
-0.4787
2.5738
3.348
-0.0084
0.1229
0.1967
-0.0244
0.1063
0.102
0.0399
0.3902
-0.0979
0.1121
-0.003
0.0091
0.1002
0.0645
0.1253
39.651
31.387
10.123
9
22.2025
-8.5522
-2.4588
9.0453
-1.3128
-2.4019
-0.0354
-0.3905
-0.2392
0.3372
0.3366
0.739
0.0152
0.3908
-0.3012
0.1392
0.0294
0.0363
0.1294
-0.0001
0.1038
11.956
41.046
13.664
10
12.3583
-5.7779
2.7707
3.5687
-3.4923
-5.0006
0.2535
0.3763
0.5305
-0.2067
-0.2064
0.0558
0.347
0.1219
-0.0471
0.1419
0.0129
-0.0009
0.1137
-0.0273
0.1227
13.451
39.795
9.348
11
15.2569
-2.9755
-0.0543
0.2133
0.0337
-0.7091
0.0485
0.0599
-0.6301
-0.056
-0.0797
0.1139
-0.0657
0.0985
0.0312
0.1223
0.0353
-0.0015
0.06
0.0066
0.1335
28.223
28.417
3.289
12
14.687
-1.9043
-1.5355
-0.9762
-0.5946
3.2923
0.0888
0.0836
0.0752
-0.3236
-0.0203
-0.0323
-0.039
-0.0825
-0.0685
0.171
0.0114
0.0164
0.0579
-0.0015
0.0849
26.434
31.925
3.075
13
3.9366
2.4846
-7.4517
5.911
-6.9721
10.7189
0.3096
-0.0394
0.1546
0.1071
0.2863
0.3647
-0.3151
0.0669
-0.5959
0.0549
0.013
0.011
0.0664
0.056
0.1867
1.862
36.843
18.915
14
12.081
-6.6674
2.6472
7.0198
0.5425
4.8311
-0.1354
0.3405
0.0785
-0.0191
0.0152
0.2267
0.2647
0.5839
0.1202
0.0829
0.0422
0.0263
0.1188
0.0683
0.1105
3.255
23.355
24.526
15
0.8357
0.8751
-3.2857
1.848
-2.6647
4.2788
-0.0021
-0.1184
0.0953
-0.1958
0.0827
0.4063
0.1411
0.2714
-0.0806
0.0918
0.0387
-0.0035
0.1083
0.056
0.1535
4.012
28.362
25.847
16
2.0679
-1.7323
0.9909
5.688
-6.9264
11.6483
-0.0319
0.1384
-0.3445
-0.099
-0.44
0.0341
-0.0957
0.6393
0.4719
0.0852
0.0388
0.0679
0.126
0.0424
0.0945
38.399
25.179
9.192
17
5.7998
-2.8917
-3.7117
4.6523
1.4829
5.5792
-0.2664
0.1684
0.8368
0.3561
0.0648
-0.4754
-0.0177
-0.105
0.2016
0.0407
-0.0226
-0.061
0.0681
0.0367
0.1977
37.559
24.117
24.134
18
0.2546
-0.7373
1.0323
2.3311
0.0658
1.1152
-0.0016
0.0331
0.039
-0.0566
-0.0567
-0.2989
0.0169
-0.013
0.0583
0.0863
0.0138
0.0189
0.1071
0.0271
0.128
35.904
21.531
18.467
19
4.724
-4.706
4.93
3.4923
-4.583
6.7657
0.2244
0.2757
0.1665
-0.1361
-0.191
0.0897
0.3284
0.3608
-0.0334
0.1101
0.002
-0.0153
0.0844
0.0345
0.1039
10.475
29.277
12.197
20
-1.0054
0.3116
-0.6036
0.9171
-0.5759
3.5094
-0.1354
0.1153
-0.0012
-0.013
0.0801
0.2485
-0.1377
0.0969
0.0553
0.127
-0.0245
-0.0151
0.1051
0.0327
0.1388
29.072
33.279
14.388
21
2.8195
-2.5253
-2.0155
1.2058
-0.6945
0.3113
-0.2482
-0.3975
0.0466
0.0028
0.2238
0.2578
-0.0626
0.0765
0.0244
0.133
0.0428
0.0146
0.1389
-0.0028
0.093
12.044
28.987
27.36
22
1.9219
-1.392
0.8948
1.3292
-0.2796
1.2738
-0.0534
-0.0041
-0.0884
-0.044
0.0008
-0.0354
0.032
-0.0627
0.0527
0.1167
0.0035
-0.0005
0.0983
0.0087
0.1087
28.715
19.32
19.412
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 5
2
X-RAY DIFFRACTION
1
A
94 - 99
3
X-RAY DIFFRACTION
2
B
1 - 5
4
X-RAY DIFFRACTION
2
B
94 - 99
5
X-RAY DIFFRACTION
3
A
6 - 10
6
X-RAY DIFFRACTION
4
B
6 - 10
7
X-RAY DIFFRACTION
5
A
22 - 32
8
X-RAY DIFFRACTION
6
A
33 - 43
9
X-RAY DIFFRACTION
7
B
22 - 32
10
X-RAY DIFFRACTION
8
B
33 - 43
11
X-RAY DIFFRACTION
9
A
44 - 49
12
X-RAY DIFFRACTION
10
A
52 - 56
13
X-RAY DIFFRACTION
11
B
44 - 49
14
X-RAY DIFFRACTION
12
B
52 - 56
15
X-RAY DIFFRACTION
13
A
57 - 62
16
X-RAY DIFFRACTION
14
A
63 - 68
17
X-RAY DIFFRACTION
15
A
69 - 76
18
X-RAY DIFFRACTION
16
B
57 - 62
19
X-RAY DIFFRACTION
17
B
63 - 68
20
X-RAY DIFFRACTION
18
B
69 - 76
21
X-RAY DIFFRACTION
19
A
77 - 85
22
X-RAY DIFFRACTION
20
B
77 - 85
23
X-RAY DIFFRACTION
21
A
86 - 93
24
X-RAY DIFFRACTION
22
B
86 - 93
+
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