Method to determine structure: SAD / Resolution: 2.343→42.991 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.159 / SU ML: 0.163 / Cross valid method: FREE R-VALUE / ESU R: 0.204 / ESU R Free: 0.182 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2474
540
5.004 %
Rwork
0.2184
10251
-
all
0.22
-
-
obs
-
10791
99.741 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 71.975 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.236 Å2
0 Å2
0 Å2
2-
-
-2.236 Å2
0 Å2
3-
-
-
4.472 Å2
Refinement step
Cycle: LAST / Resolution: 2.343→42.991 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
962
0
5
8
975
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.013
967
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
883
X-RAY DIFFRACTION
r_angle_refined_deg
1.842
1.629
1322
X-RAY DIFFRACTION
r_angle_other_deg
1.408
1.588
2038
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.228
5
134
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
44.297
24.783
46
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.168
15
141
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
24.187
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.073
0.2
149
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.02
1130
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
177
X-RAY DIFFRACTION
r_nbd_refined
0.236
0.2
162
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.194
0.2
739
X-RAY DIFFRACTION
r_nbtor_refined
0.16
0.2
473
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.09
0.2
481
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.218
0.2
15
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.035
0.2
1
X-RAY DIFFRACTION
r_metal_ion_refined
0.009
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.284
0.2
9
X-RAY DIFFRACTION
r_nbd_other
0.193
0.2
66
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.408
0.2
2
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.117
0.2
1
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
0.009
0.2
1
X-RAY DIFFRACTION
r_mcbond_it
6.405
7.444
542
X-RAY DIFFRACTION
r_mcbond_other
6.405
7.443
541
X-RAY DIFFRACTION
r_mcangle_it
9.173
11.139
674
X-RAY DIFFRACTION
r_mcangle_other
9.169
11.141
675
X-RAY DIFFRACTION
r_scbond_it
9.194
8.125
425
X-RAY DIFFRACTION
r_scbond_other
9.185
8.129
426
X-RAY DIFFRACTION
r_scangle_it
12.535
11.868
648
X-RAY DIFFRACTION
r_scangle_other
12.525
11.873
649
X-RAY DIFFRACTION
r_lrange_it
14.878
88.612
950
X-RAY DIFFRACTION
r_lrange_other
14.871
88.66
951
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
2.343-2.403
0.407
38
0.365
712
0.367
773
0.85
0.816
97.0246
0.349
2.403-2.469
0.344
37
0.344
722
0.344
759
0.858
0.815
100
0.32
2.469-2.54
0.372
37
0.29
700
0.294
737
0.803
0.856
100
0.256
2.54-2.618
0.44
36
0.306
683
0.312
719
0.788
0.852
100
0.274
2.618-2.704
0.456
35
0.286
655
0.294
690
0.836
0.881
100
0.25
2.704-2.798
0.3
34
0.273
651
0.274
685
0.872
0.871
100
0.244
2.798-2.903
0.3
33
0.282
623
0.283
656
0.839
0.85
100
0.246
2.903-3.021
0.303
31
0.272
601
0.273
632
0.877
0.867
100
0.242
3.021-3.155
0.368
31
0.264
575
0.268
606
0.829
0.884
100
0.241
3.155-3.308
0.303
30
0.235
566
0.239
596
0.9
0.915
100
0.222
3.308-3.486
0.302
27
0.224
514
0.228
541
0.904
0.928
100
0.214
3.486-3.696
0.275
26
0.224
508
0.226
534
0.931
0.945
100
0.218
3.696-3.949
0.178
25
0.199
471
0.198
496
0.961
0.955
100
0.2
3.949-4.262
0.181
24
0.173
445
0.173
469
0.957
0.969
100
0.18
4.262-4.665
0.162
21
0.142
413
0.143
434
0.981
0.976
100
0.153
4.665-5.208
0.201
21
0.164
388
0.166
409
0.963
0.965
100
0.175
5.208-5.999
0.22
17
0.23
336
0.23
353
0.955
0.938
100
0.243
5.999-7.311
0.258
16
0.239
298
0.24
314
0.944
0.94
100
0.259
7.311-10.193
0.2
12
0.165
236
0.166
248
0.972
0.973
100
0.196
10.193-42.991
0.264
9
0.285
154
0.284
165
0.976
0.938
98.7879
0.334
+
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