Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.918 Å / Relative weight: 1
Reflection
Resolution: 1.9→25 Å / Num. obs: 91520 / % possible obs: 97.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shell
Resolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 5 / Num. unique obs: 12289 / % possible all: 91.6
-
Processing
Software
Name
Version
Classification
MxCuBE
datacollection
MOLREP
phasing
REFMAC
5
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.901 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21022
1829
2 %
RANDOM
Rwork
0.1689
-
-
-
obs
0.16972
89514
97.39 %
-
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: 20.345 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.54 Å2
0 Å2
0 Å2
2-
-
-0.6 Å2
0 Å2
3-
-
-
0.06 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7386
0
0
923
8309
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.02
7698
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.005
1.943
10530
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.985
5
969
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.398
24.324
377
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.147
15
1213
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.225
15
50
X-RAY DIFFRACTION
r_chiral_restr
0.165
0.2
1117
X-RAY DIFFRACTION
r_gen_planes_refined
0.012
0.021
6050
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
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.9→1.945 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.256
107
-
Rwork
0.223
5588
-
obs
-
-
86.96 %
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
2.1969
-0.531
-0.4064
2.7637
0.408
0.338
0.0496
0.0351
0.0707
-0.1269
-0.008
0.2635
-0.002
-0.0684
-0.0416
0.0544
0.0142
-0.025
0.0675
0.023
0.0521
27.3524
84.303
73.0359
2
2.8452
0.868
1.3496
4.5537
-0.5728
8.1107
-0.0578
-0.0681
0.2543
-0.1869
0.039
-0.1591
-0.0835
0.4426
0.0188
0.0698
-0.0252
0.0193
0.0969
-0.0058
0.0477
44.3025
92.7434
76.4072
3
0.1452
0.0442
-0.086
1.0071
0.0532
1.1235
0.0295
0.0332
0.0572
0.0544
-0.0402
-0.0039
-0.1416
0.1023
0.0107
0.0514
-0.0058
0.0102
0.0529
0.0085
0.0312
37.9574
91.5985
82.028
4
1.201
-0.5672
0.6486
1.925
-1.0766
1.5156
0.032
0.0055
0.1377
-0.0687
0.0107
-0.0322
-0.0829
0.0765
-0.0427
0.0544
-0.0154
0.0183
0.0131
-0.008
0.0295
36.2984
94.2114
83.7549
5
0.9446
-1.1637
0.4444
5.769
-1.3294
0.9196
-0.0247
-0.1444
0.0762
0.0544
0.1015
-0.1865
-0.0415
0.0703
-0.0768
0.0367
-0.012
0.0153
0.07
-0.0341
0.0448
39.4822
86.7718
90.4428
6
0.4885
0.2172
-0.2683
1.0955
-0.2732
0.6538
0.0161
0.0653
0.011
-0.0438
-0.0108
0.153
0.0072
-0.0686
-0.0053
0.0219
0.0057
-0.0094
0.042
-0.0004
0.0251
28.0306
80.407
79.5874
7
6.1372
0.9657
-2.4906
5.5023
1.388
2.8029
0.0206
-0.0785
-0.1211
0.0485
-0.0914
-0.0711
0.2543
0.002
0.0708
0.0719
0.0179
0.0008
0.0464
0.0199
0.0283
38.8857
63.0428
87.6169
8
0.7968
-0.0065
-0.0189
0.4647
-0.1626
0.5147
0.0163
0.0079
-0.0119
-0.073
0.0041
0.0143
0.1123
-0.0006
-0.0204
0.0597
0.0021
-0.0139
0.042
-0.0042
0.0095
34.2194
72.4713
81.5784
9
14.8502
-0.0432
-3.8262
5.1468
2.5936
6.8453
0.0756
-0.3277
0.1607
0.0568
-0.2018
0.7695
-0.0481
-0.3455
0.1262
0.0048
-0.0039
0.0031
0.1006
-0.0255
0.1603
16.969
79.3724
84.1622
10
0.319
-0.1388
-0.1669
1.1361
0.1912
0.9727
0.0335
-0.0509
0.0033
-0.0226
0.0174
0.0434
0.0303
0.0034
-0.0509
0.0146
0.0029
0.0031
0.0471
-0.0003
0.0296
32.8513
78.1677
87.8414
11
1.633
1.194
-0.0639
1.6427
0.6813
1.8291
0.0262
-0.0496
-0.0028
0.198
-0.0431
0.1537
0.064
-0.0661
0.0169
0.0734
-0.0026
0.0378
0.0484
0.0078
0.051
30.1897
63.0624
130.8798
12
1.6936
-0.5125
-1.1899
7.1444
2.586
14.8477
-0.1713
0.0648
0.0754
0.4636
0.3721
-0.5405
0.4854
0.7846
-0.2008
0.072
0.0446
-0.0269
0.0739
-0.0245
0.0585
46.9247
54.7397
126.3076
13
0.7717
-0.3274
-0.4261
1.7748
-0.0234
0.9761
-0.0439
0.0139
-0.0079
-0.0939
0.0136
-0.0712
0.1341
0.1048
0.0303
0.0686
0.0031
0.0225
0.0414
-0.0056
0.027
40.8683
56.5374
116.8115
14
0.6057
0.0403
0.7705
1.1682
0.335
1.0596
0.0915
-0.0908
-0.054
0.1885
-0.0398
0.0057
0.1829
-0.1149
-0.0517
0.095
0.0033
0.0169
0.0485
0.0127
0.0345
38.5639
53.7727
129.4777
15
1.1063
0.4509
-0.7713
2.5518
-0.6963
2.5675
-0.0683
-0.0263
-0.0668
-0.0247
-0.0143
-0.1188
0.1919
0.0147
0.0825
0.0168
0.0066
0.003
0.015
-0.0053
0.0112
39.3649
54.8287
118.1929
16
2.6489
-2.332
-0.1971
4.5966
1.9509
1.2655
0.1191
0.2102
0.2253
-0.2092
-0.0202
-0.2934
-0.1041
0.1104
-0.0989
0.0882
-0.0119
0.0445
0.0779
0.0105
0.0443
43.6815
69.8178
110.035
17
0.8016
0.104
-0.1805
2.267
0.561
0.6766
-0.0061
0.0251
-0.0427
-0.1272
-0.0262
0.2306
0.0962
-0.1363
0.0323
0.0471
-0.0258
-0.0182
0.0466
0.0008
0.0412
27.285
58.2064
117.6125
18
0.3785
-0.4967
0.555
1.248
-1.0283
1.3731
0.0356
-0.0295
0.0401
0.0912
-0.0323
0.0937
-0.0297
0.014
-0.0033
0.0728
-0.0026
0.0287
0.0568
-0.0179
0.0435
35.406
70.8015
128.837
19
4.4362
2.0159
0.4541
3.0162
0.434
2.6307
0.0222
-0.066
-0.0064
0.0023
0.0345
-0.0357
-0.1644
-0.0067
-0.0568
0.07
-0.0062
0.0296
0.0116
0.0047
0.0214
40.4077
84.0606
115.1663
20
0.3563
0.0964
0.2077
1.3937
0.1634
0.7509
0.0161
-0.0132
0.0361
-0.0083
-0.0239
0.1128
-0.0816
-0.043
0.0077
0.0277
-0.0036
0.0172
0.0431
-0.0067
0.0254
33.3426
70.8406
118.0717
21
1.0187
-0.1573
-0.4203
0.5768
0.065
0.5179
-0.0105
0.0519
0.0542
-0.0149
-0.0519
-0.0211
0.0295
0.0559
0.0624
0.0162
-0.0004
0.0111
0.032
0.0164
0.0472
65.0866
100.3715
103.8197
22
2.3402
0.337
0.456
0.5368
0.1679
0.8929
-0.0304
0.202
0.0639
-0.1124
-0.0141
-0.0457
0.0517
0.0659
0.0445
0.0347
0.0096
0.0248
0.0232
0.0086
0.0475
64.666
95.9895
98.7296
23
12.6146
4.0063
0.5188
14.4709
-0.8562
15.4246
0.2757
-0.0402
0.9287
-0.2797
-0.2281
0.5858
-0.7368
-0.8548
-0.0476
0.0932
0.0444
-0.011
0.0536
-0.0008
0.0936
42.4454
99.1785
100.6614
24
1.2557
-0.5304
0.1226
0.5034
0.1415
0.4353
-0.0018
0.0115
-0.0749
-0.0352
-0.0005
-0.041
0.1013
0.032
0.0023
0.0611
0.0103
0.0302
0.0314
0.0117
0.0575
67.0331
90.5037
103.9192
25
3.3935
-3.0808
-1.0734
8.6764
2.3901
1.2207
-0.1546
-0.0189
-0.4439
-0.1991
0.0074
0.1991
0.0556
0.0278
0.1472
0.0937
-0.0383
0.0475
0.0878
0.0487
0.1186
52.944
84.9632
119.1068
26
1.2227
0.3093
-1.1516
1.1707
-0.5343
1.6282
0.0965
-0.1785
0.1007
0.0487
-0.0776
0.0343
-0.0179
0.0846
-0.0189
0.0253
-0.0257
0.0167
0.0517
-0.019
0.0572
60.0801
105.3463
115.6482
27
2.7665
-1.3558
-0.7614
4.1485
1.532
1.2757
0.0308
-0.0806
0.0277
-0.0176
-0.1179
0.1607
0.0234
-0.0485
0.0871
0.0222
-0.023
0.0238
0.0354
-0.0254
0.051
41.6685
95.8841
114.2583
28
2.7837
-1.0932
-2.848
3.0597
0.0981
3.3638
0.0545
-0.0588
0.0206
0.0868
-0.0653
0.0359
-0.0774
0.0369
0.0109
0.0167
-0.0322
0.0073
0.0798
-0.0374
0.059
54.1284
102.8009
116.8156
29
1.7239
-1.1329
-1.3513
18.5906
-3.0291
11.2836
-0.0431
-0.2744
-0.0141
0.5178
-0.3196
-0.6298
0.7803
0.5252
0.3627
0.1745
0.0201
-0.0168
0.1323
0.0608
0.0531
63.1651
85.7314
120.6222
30
0.9777
-0.2184
-0.5485
1.4341
1.1207
1.2751
-0.003
-0.0579
-0.084
0.003
-0.0856
0.079
0.0273
-0.0568
0.0886
0.0267
-0.0125
0.0165
0.0238
0.0006
0.0377
52.8411
93.412
110.2759
31
0.5487
0.8841
0.7886
2.623
0.2739
2.6178
-0.0283
0.1595
0.0013
-0.237
-0.194
-0.1826
-0.0153
0.4327
0.2223
0.0818
0.095
0.0686
0.2621
0.0479
0.1494
65.9583
47.2941
84.1294
32
0.9476
-0.0689
0.5675
0.9472
-0.9257
1.3042
-0.0473
0.0131
0.0045
0.0741
-0.1191
-0.1376
-0.036
0.1688
0.1664
0.0392
0.0152
0.0261
0.0581
0.0616
0.1234
64.297
47.4506
100.4305
33
8.4963
6.6008
-3.9102
18.4716
2.3137
3.9469
-0.0346
-0.6637
-0.3703
-0.5423
0.0948
-0.8278
-0.1896
0.5454
-0.0602
0.0686
0.0522
0.0434
0.2891
0.1826
0.2658
78.113
45.0083
92.2937
34
1.8308
-0.6325
0.5165
0.9853
-0.8285
2.3074
-0.0309
-0.2714
0.0004
0.2189
-0.0031
-0.0226
-0.136
-0.1918
0.034
0.093
-0.0037
0.0193
0.093
0.0194
0.0835
53.9343
52.5951
103.4061
35
0.9887
0.2152
0.3262
0.8078
-0.2555
0.4348
0.0045
0.1301
0.1377
0.0854
-0.0957
-0.2182
-0.1034
0.1245
0.0913
0.0348
-0.0277
-0.0076
0.1043
0.0945
0.1522
69.5524
57.3497
95.4671
36
2.5639
1.2438
-0.598
2.0061
-2.4548
3.7542
-0.0088
0.0439
0.3545
-0.0118
-0.134
0.0345
-0.2154
0.0909
0.1428
0.1943
0.1049
-0.0186
0.1408
0.06
0.1242
51.4194
61.8023
82.6613
37
1.5912
-0.4925
0.8195
1.6883
-0.2616
0.7569
0.0498
0.2463
-0.1914
-0.2462
-0.0819
0.0008
0.1248
0.1616
0.0322
0.103
0.0614
0.0482
0.0898
-0.0079
0.0769
57.3883
42.5293
85.163
38
1.1455
-0.6353
0.4468
2.4914
0.9299
2.7344
0.1336
0.0548
-0.1705
-0.1907
-0.0649
0.2391
0.06
-0.2057
-0.0687
0.0283
0.0068
-0.0302
0.0396
-0.0085
0.0637
42.312
48.774
85.8149
39
1.766
0.1483
0.8314
1.384
0.3262
1.8734
0.0889
0.3167
0.0304
-0.1656
-0.1981
0.0587
-0.0717
0.2932
0.1092
0.0803
0.0509
0.0346
0.131
0.0324
0.0611
57.9908
52.6988
85.1172
40
1.4343
-0.5964
0.9051
0.6707
-0.0176
1.8341
0.0243
0.0566
-0.041
-0.015
-0.0985
-0.0372
-0.0572
-0.0355
0.0742
0.0379
0.0171
0.0149
0.0223
0.0184
0.0502
51.7251
53.7763
91.0066
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 17
2
X-RAY DIFFRACTION
2
A
18 - 23
3
X-RAY DIFFRACTION
3
A
24 - 64
4
X-RAY DIFFRACTION
4
A
65 - 84
5
X-RAY DIFFRACTION
5
A
85 - 101
6
X-RAY DIFFRACTION
6
A
102 - 154
7
X-RAY DIFFRACTION
7
A
155 - 165
8
X-RAY DIFFRACTION
8
A
166 - 191
9
X-RAY DIFFRACTION
9
A
192 - 198
10
X-RAY DIFFRACTION
10
A
199 - 235
11
X-RAY DIFFRACTION
11
B
1 - 17
12
X-RAY DIFFRACTION
12
B
18 - 23
13
X-RAY DIFFRACTION
13
B
24 - 51
14
X-RAY DIFFRACTION
14
B
52 - 64
15
X-RAY DIFFRACTION
15
B
65 - 86
16
X-RAY DIFFRACTION
16
B
87 - 94
17
X-RAY DIFFRACTION
17
B
95 - 123
18
X-RAY DIFFRACTION
18
B
124 - 154
19
X-RAY DIFFRACTION
19
B
155 - 165
20
X-RAY DIFFRACTION
20
B
166 - 235
21
X-RAY DIFFRACTION
21
C
1 - 64
22
X-RAY DIFFRACTION
22
C
65 - 85
23
X-RAY DIFFRACTION
23
C
86 - 89
24
X-RAY DIFFRACTION
24
C
90 - 114
25
X-RAY DIFFRACTION
25
C
115 - 125
26
X-RAY DIFFRACTION
26
C
126 - 152
27
X-RAY DIFFRACTION
27
C
153 - 172
28
X-RAY DIFFRACTION
28
C
173 - 191
29
X-RAY DIFFRACTION
29
C
192 - 198
30
X-RAY DIFFRACTION
30
C
199 - 234
31
X-RAY DIFFRACTION
31
D
1 - 17
32
X-RAY DIFFRACTION
32
D
18 - 63
33
X-RAY DIFFRACTION
33
D
64 - 71
34
X-RAY DIFFRACTION
34
D
72 - 92
35
X-RAY DIFFRACTION
35
D
93 - 113
36
X-RAY DIFFRACTION
36
D
114 - 126
37
X-RAY DIFFRACTION
37
D
127 - 154
38
X-RAY DIFFRACTION
38
D
155 - 180
39
X-RAY DIFFRACTION
39
D
181 - 198
40
X-RAY DIFFRACTION
40
D
199 - 234
+
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