Resolution: 1.85→50 Å / Num. obs: 39086 / % possible obs: 99.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Χ2: 1.847 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
1.85-1.92
6.1
0.598
3868
0.96
100
1.92-1.99
6.1
0.377
3860
0.963
100
1.99-2.08
6.1
0.227
3842
0.989
100
2.08-2.19
6.1
0.152
3878
1.033
100
2.19-2.33
6.1
0.108
3857
1.157
100
2.33-2.51
6.1
0.086
3904
1.254
100
2.51-2.76
6.1
0.069
3910
1.628
100
2.76-3.16
6
0.065
3929
2.754
100
3.16-3.99
5.8
0.049
3966
3.452
100
3.99-50
5.6
0.043
4072
4.441
97.6
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.004
dataextraction
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
SHELX
phasing
MLPHARE
phasing
DM
phasing
ARP/wARP
modelbuilding
Coot
modelbuilding
Refinement
Resolution: 1.85→33.81 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.469 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.259
1957
5 %
RANDOM
Rwork
0.221
-
-
-
obs
0.223
39025
99.75 %
-
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: 35.309 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.02 Å2
0 Å2
0 Å2
2-
-
0.02 Å2
0 Å2
3-
-
-
-0.04 Å2
Refinement step
Cycle: LAST / Resolution: 1.85→33.81 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3153
0
0
183
3336
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
3268
X-RAY DIFFRACTION
r_angle_refined_deg
1.097
1.958
4453
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.141
5
414
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.764
25.302
149
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.955
15
569
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.715
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.08
0.2
530
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2430
X-RAY DIFFRACTION
r_mcbond_it
0.509
1.5
2018
X-RAY DIFFRACTION
r_mcangle_it
0.869
2
3252
X-RAY DIFFRACTION
r_scbond_it
1.599
3
1250
X-RAY DIFFRACTION
r_scangle_it
2.431
4.5
1192
LS refinement shell
Resolution: 1.85→1.898 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.322
140
-
Rwork
0.282
2708
-
all
-
2848
-
obs
-
-
99.72 %
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
13.1229
4.3499
-5.2827
2.513
-4.6352
9.9382
-0.1583
0.8039
-0.1494
-0.1622
0.098
-0.07
0.5087
0.0712
0.0603
0.4934
0.0138
-0.1325
0.1961
-0.0091
0.2441
51.353
-2.6336
15.1878
2
8.4381
-1.8976
9.6929
7.7857
-1.1604
29.2496
0.1618
0.5508
0.1906
-0.1324
-0.3883
-0.0227
-0.0741
0.1078
0.2265
0.0888
-0.0041
-0.0054
0.296
0.0134
0.2982
38.9413
-2.1323
12.2062
3
7.0327
-2.8543
-1.3023
5.6143
0.4069
4.9148
-0.0743
-0.2498
-0.0107
0.0772
0.1191
-0.327
-0.0617
0.4059
-0.0448
0.0416
-0.0576
-0.0091
0.194
0.0146
0.166
29.4509
3.5649
12.1313
4
6.096
-0.9432
-2.4111
3.1183
-2.6582
9.6404
-0.0251
-0.0192
0.1673
0.0587
0.0871
0.2076
-0.6978
-0.503
-0.062
0.115
0.0179
0.0074
0.1476
0.0326
0.2022
17.8506
9.2607
8.49
5
19.7114
7.6473
1.3411
2.9727
0.4955
22.6968
0.1464
-0.4597
0.9019
0.0309
-0.138
0.3251
-0.9986
0.0197
-0.0084
0.1604
-0.102
0.1149
0.1688
-0.0971
0.2382
26.7257
9.7498
5.1872
6
2.8609
0.3265
-4.5056
6.464
-0.6486
7.548
-0.0578
0.1528
-0.2036
-0.3913
-0.0186
0.1021
0.0968
-0.1321
0.0765
0.1124
-0.0049
-0.0384
0.1443
-0.0096
0.1878
25.7445
0.1846
3.4522
7
3.0272
0.5891
-2.6163
0.1678
-1.3438
15.9174
-0.0714
-0.4067
-0.2742
-0.0112
-0.1002
-0.0685
0.1594
0.4118
0.1716
0.0657
-0.0313
-0.0405
0.19
0.053
0.2981
20.2762
-2.3524
20.2728
8
2.9867
1.238
-3.0024
0.7526
-1.7708
7.0221
0.0615
-0.1561
-0.0731
0.1958
-0.2535
-0.2344
-0.0225
0.6691
0.192
0.2482
-0.0955
-0.1387
0.2627
0.1012
0.3028
16.4799
-4.3788
39.8034
9
6.8206
1.6608
-4.4005
0.9769
-2.0989
4.6984
0.0117
-0.7898
0.3222
0.2634
-0.0509
-0.0497
-0.4053
0.2593
0.0392
0.4935
-0.0609
-0.1103
0.1892
-0.0124
0.2253
9.6782
1.5574
46.4644
10
4.3446
0.1856
-0.1879
1.7051
-4.0516
9.7975
0.1558
0.0025
0.11
0.028
-0.0507
-0.0305
-0.0843
0.2312
-0.1052
0.1935
-0.1252
-0.0753
0.1994
-0.0294
0.3101
16.0268
6.7315
33.3449
11
10.9192
9.7816
1.1562
16.539
4.0579
1.3118
0.1772
-0.0871
0.4296
0.1113
-0.0462
-0.0015
-0.0666
0.0494
-0.131
0.293
-0.1507
0.0614
0.1911
0.0251
0.172
15.1344
6.7752
19.644
12
14.6996
-1.6001
-0.4522
10.5202
1.5403
9.3765
0.1501
-0.08
0.1979
0.1963
0.0678
0.0228
-0.6582
0.2715
-0.2179
0.0935
0.0313
-0.0161
0.1193
0.0041
0.1294
7.4864
3.8666
16.287
13
3.5725
1.2966
1.8701
6.5761
-1.0691
20.6953
0.0334
0.0696
-0.2335
-0.0544
-0.1095
-0.0748
-0.069
-0.0053
0.0761
0.0023
0.0012
-0.0021
0.0527
0.0142
0.1807
9.846
-3.538
16.5203
14
6.0928
0.9369
-7.4939
0.1609
-1.6615
24.6858
-0.0434
0.1236
-0.4929
-0.0137
0.0126
-0.0572
0.2214
-0.0064
0.0308
0.0569
-0.0184
-0.0308
0.0714
0.0473
0.1992
9.0406
-5.3679
28.7732
15
5.3416
3.0651
-1.4006
3.9743
-4.5242
10.0869
0.0198
-0.175
-0.1328
0.3223
-0.2113
-0.3938
0.0129
0.5099
0.1915
0.1683
0.0017
-0.0656
0.0875
0.004
0.1628
7.0916
-9.3551
41.3264
16
2.8309
10.8378
7.7032
42.4531
29.4549
20.963
-0.0721
-0.0929
0.0443
0.227
-0.0408
0.4204
-0.2219
-0.2559
0.1129
0.43
0.055
0.0376
0.238
0.0691
0.2045
3.9318
-12.4175
48.5716
17
1.1883
0.066
0.6813
10.8008
-2.9914
1.8792
-0.0475
0.0973
-0.1043
0.0614
0.0276
-0.0265
-0.1012
-0.0597
0.0199
0.0823
0.0025
-0.0079
0.1005
-0.0044
0.1006
0.8046
-3.6231
36.3596
18
17.5347
1.968
9.2584
5.6378
-4.8165
11.2205
-0.6656
0.9158
0.5999
-0.1081
-0.1705
-0.4285
-0.324
0.7873
0.8361
0.2511
-0.1018
-0.0772
0.1834
0.0778
0.3224
8.4853
11.8616
31.3174
19
4.5825
-1.2923
-1.5821
11.1364
8.8873
13.3712
0.0517
0.3771
0.1296
-0.825
-0.0801
-0.3243
-0.5331
0.1814
0.0284
0.3157
-0.0805
-0.0429
0.3347
0.1167
0.3709
9.3171
18.6236
31.4907
20
1.7153
1.3069
-0.9646
5.6699
-2.6108
2.2662
0.0474
-0.1464
0.1766
0.3317
-0.1728
-0.133
-0.1802
0.2156
0.1254
0.2731
-0.0267
-0.0373
0.162
-0.0199
0.1287
2.2026
7.7881
43.8612
21
28.302
-14.1195
18.3794
7.0499
-9.1713
11.9371
-0.0698
-1.9073
-1.5487
0.0274
1.0466
0.7996
-0.0726
-1.268
-0.9767
0.4337
0.1206
-0.33
1.2447
-0.0461
0.5987
-13.7181
16.4403
-3.4847
22
8.7552
-6.1216
7.0318
15.6802
-7.2375
6.1257
-0.0845
-0.326
-0.2201
-0.2041
0.367
0.8625
-0.0019
-0.3415
-0.2825
0.1782
-0.1166
0.0466
0.5521
-0.2913
0.2647
-9.5092
9.581
-0.7158
23
10.2707
-1.0322
-0.4397
9.229
3.3121
8.2656
0.0371
0.1457
-0.8148
0.2428
-0.056
0.095
0.7448
-0.1473
0.0189
0.172
0.0236
-0.0199
0.1886
-0.0071
0.1342
0.1576
5.3858
4.218
24
14.2667
7.3749
-5.2986
7.2579
-0.9096
10.7085
0.0546
0.5745
-0.6217
-0.503
-0.0002
-0.3356
0.6339
-0.0602
-0.0544
0.2096
0.0541
0.0042
0.2641
-0.0729
0.147
-0.1443
7.5843
-5.7982
25
9.9128
5.0832
-6.2236
14.8755
-0.613
9.2551
0.3499
0.5807
0.0235
-0.6971
-0.57
0.0856
-0.5465
-0.363
0.2201
0.3025
0.0365
-0.0679
0.4247
0.0057
0.1608
-4.3563
12.0117
-9.3225
26
9.9663
-7.9553
1.4759
6.4113
-2.0759
13.7271
0.8138
0.7863
0.1949
-0.611
-0.5893
-0.1306
-0.5246
-0.0988
-0.2245
0.4276
-0.0354
-0.0591
0.3223
0.0441
0.2112
-2.0344
17.3099
-3.0107
27
5.525
-1.2431
-3.0692
4.6984
3.83
9.6971
0.0126
0.3541
0.0612
-0.2297
0.0087
0.1717
-0.2552
-0.6047
-0.0212
0.113
0.0409
-0.033
0.1212
-0.0179
0.1071
-5.761
16.9321
7.7885
28
14.4316
-1.7642
-3.2124
8.4647
-6.0188
20.0316
-0.6128
0.2369
0.3214
-1.1205
0.0955
0.4324
-0.2669
-1.5242
0.5173
0.342
0.0976
-0.1155
0.2657
-0.0437
0.273
-13.1427
17.9536
16.471
29
5.7068
-1.304
-8.149
1.1135
0.338
23.433
-0.1621
0.1428
-0.2202
-0.0197
-0.3123
0.3689
-0.1067
-0.2931
0.4743
0.2768
0.0374
0.0221
0.3448
-0.0037
0.3525
-17.3613
18.2473
26.6062
30
11.7697
-3.5174
0.1828
17.5767
-3.1496
12.7458
-0.0458
0.0055
-0.0971
0.1191
-0.0834
0.4558
-0.1248
-1.0126
0.1292
0.1997
-0.0284
0.0674
0.2811
-0.0382
0.2562
-18.8829
15.4048
38.3789
31
5.6967
1.0933
-1.7825
1.9033
5.2802
19.3561
0.0837
-0.2147
-0.0868
0.1888
-0.0915
0.0456
0.48
-0.1082
0.0078
0.1624
0.0082
0.0855
0.1976
0.0331
0.3887
-15.2868
7.942
33.0992
32
3.469
0.5069
-3.1935
0.673
1.7184
16.2197
-0.0844
0.5068
0.1433
-0.192
-0.0557
0.2856
-0.3795
-0.6152
0.14
0.1815
0.033
-0.0317
0.307
0.0172
0.3162
-12.4865
6.4676
19.8718
33
13.382
3.7544
1.6231
8.5983
0.2843
4.2771
-0.1697
0.1933
-0.1639
0.1576
0.0419
0.0584
0.5019
-0.0981
0.1278
0.1328
0.0074
-0.0146
0.0875
0.0132
0.0906
-1.4015
7.9281
13.4889
34
9.8889
-3.8456
-4.3702
4.5652
2.8825
6.5471
0.0691
0.0885
-0.0536
0.2946
-0.004
-0.5009
-0.1656
0.3396
-0.0651
0.0969
0.0077
-0.0405
0.0713
-0.0216
0.1669
3.512
16.0952
15.1974
35
6.076
1.4259
-5.7334
8.0723
-2.9983
18.9834
0.072
-0.0751
0.1615
0.1085
-0.1346
-0.2516
-0.2058
0.3436
0.0627
0.1134
0.0298
-0.027
0.0656
-0.0242
0.1281
-3.8191
18.3888
23.8697
36
5.2127
-1.6729
-4.4013
4.3561
3.0493
7.9545
0.041
-0.163
0.1543
0.3597
-0.0855
0.482
-0.056
-0.2547
0.0445
0.2077
-0.0023
0.0314
0.1433
-0.0036
0.2274
-11.3599
21.5198
37.9691
37
0.3654
-0.0146
1.005
4.1585
0.933
3.026
-0.0449
0.0313
-0.0555
0.5289
0.279
-0.0196
0.0412
0.2176
-0.2341
0.2715
0.0201
-0.012
0.2297
-0.0508
0.3081
-4.7464
23.695
41.5763
38
3
1.5676
0.9822
10.3001
6.1722
5.5744
-0.0636
0.1468
0.096
-0.1486
0.0592
-0.0707
-0.2667
0.12
0.0044
0.1113
-0.0012
-0.0056
0.0742
0.042
0.1007
-3.5913
7.7679
30.3673
39
4.4877
0.3181
-1.457
8.7302
-2.9747
8.5322
-0.017
0.123
-0.6287
-0.0723
0.0937
-0.0106
0.8164
-0.3549
-0.0767
0.1882
-0.074
-0.0216
0.214
-0.034
0.2439
-7.9605
-8.3738
28.4225
40
1.3286
-0.5613
-0.184
7.3891
4.9102
5.0101
0.0478
-0.1085
0.0538
0.458
-0.172
0.3045
-0.1219
-0.2789
0.1242
0.1974
-0.0136
0.0476
0.1693
0.0281
0.1568
-8.9154
5.0111
40.3375
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
14 - 19
2
X-RAY DIFFRACTION
2
A
20 - 25
3
X-RAY DIFFRACTION
3
A
26 - 36
4
X-RAY DIFFRACTION
4
A
37 - 50
5
X-RAY DIFFRACTION
5
A
51 - 56
6
X-RAY DIFFRACTION
6
A
57 - 73
7
X-RAY DIFFRACTION
7
A
74 - 85
8
X-RAY DIFFRACTION
8
A
86 - 102
9
X-RAY DIFFRACTION
9
A
103 - 113
10
X-RAY DIFFRACTION
10
A
114 - 123
11
X-RAY DIFFRACTION
11
A
124 - 129
12
X-RAY DIFFRACTION
12
A
130 - 134
13
X-RAY DIFFRACTION
13
A
135 - 143
14
X-RAY DIFFRACTION
14
A
144 - 151
15
X-RAY DIFFRACTION
15
A
152 - 160
16
X-RAY DIFFRACTION
16
A
161 - 165
17
X-RAY DIFFRACTION
17
A
166 - 184
18
X-RAY DIFFRACTION
18
A
185 - 189
19
X-RAY DIFFRACTION
19
A
190 - 196
20
X-RAY DIFFRACTION
20
A
197 - 217
21
X-RAY DIFFRACTION
21
B
24 - 29
22
X-RAY DIFFRACTION
22
B
30 - 35
23
X-RAY DIFFRACTION
23
B
36 - 47
24
X-RAY DIFFRACTION
24
B
48 - 54
25
X-RAY DIFFRACTION
25
B
55 - 64
26
X-RAY DIFFRACTION
26
B
65 - 71
27
X-RAY DIFFRACTION
27
B
72 - 82
28
X-RAY DIFFRACTION
28
B
83 - 87
29
X-RAY DIFFRACTION
29
B
88 - 98
30
X-RAY DIFFRACTION
30
B
99 - 106
31
X-RAY DIFFRACTION
31
B
107 - 115
32
X-RAY DIFFRACTION
32
B
116 - 123
33
X-RAY DIFFRACTION
33
B
124 - 132
34
X-RAY DIFFRACTION
34
B
133 - 143
35
X-RAY DIFFRACTION
35
B
144 - 150
36
X-RAY DIFFRACTION
36
B
151 - 164
37
X-RAY DIFFRACTION
37
B
165 - 171
38
X-RAY DIFFRACTION
38
B
172 - 190
39
X-RAY DIFFRACTION
39
B
191 - 199
40
X-RAY DIFFRACTION
40
B
200 - 217
+
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