Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 1.75→20 Å / Num. obs: 29945 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 48.8
Reflection shell
Resolution: 1.75→1.81 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 21.6 / % possible all: 64.5
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
SBC-Collect
datacollection
HKL-2000
datascaling
SOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.77→19.96 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.596 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19455
1513
5.1 %
RANDOM
Rwork
0.15805
-
-
-
obs
0.15996
28392
99.12 %
-
all
-
29945
-
-
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: 22.652 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.24 Å2
0 Å2
-1.24 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
-0.29 Å2
Refinement step
Cycle: LAST / Resolution: 1.77→19.96 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2233
0
0
264
2497
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
2277
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.415
1.967
3073
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.089
5
277
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.043
23.737
99
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.625
15
415
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.989
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.11
0.2
343
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1679
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.215
0.2
1131
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.312
0.2
1602
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.164
0.2
207
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
0.246
0.2
64
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.178
0.2
38
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
1.761
3
1443
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.573
4
2259
X-RAY DIFFRACTION
r_scbond_it
3.487
5
965
X-RAY DIFFRACTION
r_scangle_it
5.096
7
814
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.77→1.816 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.205
113
-
Rwork
0.156
2026
-
obs
-
-
96.79 %
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
37.984
8.2747
5.8881
5.305
3.0396
1.794
-0.0268
-2.6656
0.7593
0.468
-0.7039
1.1246
0.2506
-0.4992
0.7307
-0.0199
-0.01
0.0656
-0.0027
-0.0966
0.1051
-11.6967
27.4756
51.7155
2
3.5886
-0.4124
1.9579
7.9474
3.2341
2.5828
-0.0606
-0.2067
0.0645
-0.1637
-0.093
0.4442
-0.1669
-0.1897
0.1536
-0.0182
0.017
-0.0039
0.0664
0.008
0.0707
-22.4452
13.0449
41.8963
3
3.2954
0.6714
1.7986
22.2238
22.837
28.6398
-0.0248
-0.353
-0.3466
1.1163
0.4876
-0.6575
1.4044
0.3149
-0.4628
0.0136
-0.0117
-0.0107
0.0447
0.0997
-0.003
-17.3731
4.327
55.1079
4
2.1152
-0.6666
1.4714
1.7809
-0.7388
7.2802
0.0528
-0.1257
-0.1003
-0.0216
0.0908
0.0795
0.1286
0.0034
-0.1436
0.0283
-0.005
-0.0049
0.0333
0.0067
0.0721
-16.6509
8.1806
39.8354
5
10.3288
6.1678
-4.8466
4.841
-3.0471
2.2944
0.3758
-0.6878
0.4387
0.2611
-0.2614
0.2704
-0.1324
0.1243
-0.1144
-0.0095
-0.044
0.0054
0.0957
-0.0592
0.0083
-18.8027
17.9505
57.4287
6
4.4866
0.3562
-0.6369
0.8206
0.0751
1.7743
0.0012
-0.0552
0.0389
-0.0283
-0.0256
0.1507
-0.076
-0.2001
0.0244
0.0212
0.014
0.0014
0.0293
-0.0065
0.0501
-13.7563
15.6859
46.6744
7
3.5293
-2.6923
1.9641
4.0391
-2.0149
1.2275
0.1545
-0.0549
-0.1237
-0.0658
-0.0372
0.1978
0.169
-0.0611
-0.1173
0.0376
-0.0025
-0.0035
0.0189
0.0053
0.055
-1.1695
0.0598
51.3146
8
0.9004
-0.7131
0.1698
3.911
-0.0133
0.8044
0.0406
0.0437
-0.0141
-0.075
-0.0397
-0.0502
-0.0286
0.0243
-0.0009
0.0337
-0.0107
-0.002
0.0419
0.0035
0.0304
6.9061
11.2863
48.7399
9
1.0321
0.8468
1.2624
13.1928
2.4902
1.7134
0.0076
-0.1671
0.0683
0.5141
-0.0805
0.3672
0.0502
-0.158
0.073
0.0266
-0.0065
0.0178
0.0379
-0.01
0.0207
-0.3276
14.1118
58.5797
10
1.7089
-0.1626
0.7225
2.0847
-0.446
2.5716
0.0045
-0.329
0.1487
0.1944
0.0389
0.1849
-0.3087
-0.2874
-0.0434
0.0542
0.0184
0.0232
0.0645
-0.0283
0.0584
-2.0776
12.6008
53.6126
11
0.588
-0.2201
0.2588
1.6531
0.5196
1.2328
-0.0115
-0.1178
0.0318
0.0836
-0.0266
0.0406
-0.0735
-0.0873
0.0381
0.0228
-0.0018
0.0028
0.0513
-0.0082
0.0117
7.3355
14.9215
62.6778
12
2.5868
1.4857
2.5834
4.7272
1.5481
8.1581
0.0374
-0.1811
-0.0377
0.2982
-0.1773
0.1922
0.1253
-0.182
0.1399
0.0297
-0.0184
0.0151
0.0484
0.0196
0.023
7.037
5.5369
71.361
13
1.27
0.0712
0.0224
1.3261
-0.7397
2.227
0.0399
-0.0767
0.0264
0.1265
-0.1116
-0.1012
-0.0722
0.1178
0.0717
0.0262
-0.0254
-0.0127
0.0687
0.0056
0.0336
16.7515
13.0417
63.423
14
3.8342
-3.0023
-1.1947
5.0299
1.1913
3.3381
-0.0704
0.1756
-0.0662
-0.0712
0.0309
-0.2637
0.1036
0.2909
0.0395
0.0202
-0.0298
0.0218
0.1144
-0.0022
0.0738
18.6513
11.7511
47.6904
15
24.6003
0.2683
3.9199
21.5685
-2.0837
19.6004
0.3354
0.1934
-1.0956
-0.6969
-0.0966
-0.609
1.1106
0.8117
-0.2388
0.0458
0.0213
-0.0308
0.1045
0.0213
0.0058
18.9354
4.3749
69.2702
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
595 - 612
21 - 38
2
X-RAY DIFFRACTION
2
A
A
613 - 623
39 - 49
3
X-RAY DIFFRACTION
3
A
A
624 - 634
50 - 60
4
X-RAY DIFFRACTION
4
A
A
635 - 653
61 - 79
5
X-RAY DIFFRACTION
5
A
A
654 - 676
80 - 102
6
X-RAY DIFFRACTION
6
A
A
677 - 700
103 - 126
7
X-RAY DIFFRACTION
7
A
A
701 - 714
127 - 140
8
X-RAY DIFFRACTION
8
A
A
715 - 742
141 - 168
9
X-RAY DIFFRACTION
9
A
A
743 - 752
169 - 178
10
X-RAY DIFFRACTION
10
A
A
753 - 788
179 - 214
11
X-RAY DIFFRACTION
11
A
A
789 - 821
215 - 247
12
X-RAY DIFFRACTION
12
A
A
822 - 833
248 - 259
13
X-RAY DIFFRACTION
13
A
A
834 - 869
260 - 295
14
X-RAY DIFFRACTION
14
A
A
870 - 893
296 - 319
15
X-RAY DIFFRACTION
15
A
A
899 - 904
325 - 330
+
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