Resolution: 1.33→54.801 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.173 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.066 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2188
1340
4.988 %
Rwork
0.1854
25524
-
all
0.187
-
-
obs
-
26864
99.967 %
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: 23.908 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.011 Å2
0 Å2
0 Å2
2-
-
-0.011 Å2
0 Å2
3-
-
-
0.022 Å2
Refinement step
Cycle: LAST / Resolution: 1.33→54.801 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
997
0
58
138
1193
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.013
1129
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.014
994
X-RAY DIFFRACTION
r_angle_refined_deg
1.763
1.655
1522
X-RAY DIFFRACTION
r_angle_other_deg
1.545
1.597
2268
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.439
5
138
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.808
20.152
66
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.322
15
179
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.388
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
137
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
1349
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
297
X-RAY DIFFRACTION
r_nbd_refined
0.224
0.2
262
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.195
0.2
971
X-RAY DIFFRACTION
r_nbtor_refined
0.173
0.2
522
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.085
0.2
470
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.239
0.2
97
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.042
0.2
3
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.279
0.2
7
X-RAY DIFFRACTION
r_nbd_other
0.213
0.2
32
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.273
0.2
17
X-RAY DIFFRACTION
r_mcbond_it
1.896
2.146
540
X-RAY DIFFRACTION
r_mcbond_other
1.883
2.142
539
X-RAY DIFFRACTION
r_mcangle_it
2.646
3.226
682
X-RAY DIFFRACTION
r_mcangle_other
2.646
3.23
683
X-RAY DIFFRACTION
r_scbond_it
3.932
2.708
588
X-RAY DIFFRACTION
r_scbond_other
2.864
2.469
539
X-RAY DIFFRACTION
r_scangle_it
4.753
3.843
840
X-RAY DIFFRACTION
r_scangle_other
4.395
3.577
788
X-RAY DIFFRACTION
r_lrange_it
6.787
28.187
1432
X-RAY DIFFRACTION
r_lrange_other
6.115
26.462
1318
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.33-1.365
0.398
101
0.344
1842
X-RAY DIFFRACTION
99.9486
1.365-1.402
0.35
95
0.313
1802
X-RAY DIFFRACTION
100
1.402-1.443
0.297
76
0.296
1792
X-RAY DIFFRACTION
100
1.443-1.487
0.313
93
0.274
1694
X-RAY DIFFRACTION
100
1.487-1.536
0.289
93
0.256
1639
X-RAY DIFFRACTION
100
1.536-1.589
0.309
85
0.245
1621
X-RAY DIFFRACTION
100
1.589-1.649
0.245
87
0.223
1541
X-RAY DIFFRACTION
100
1.649-1.717
0.212
77
0.212
1507
X-RAY DIFFRACTION
99.9369
1.717-1.793
0.226
87
0.205
1434
X-RAY DIFFRACTION
100
1.793-1.88
0.244
58
0.207
1389
X-RAY DIFFRACTION
100
1.88-1.982
0.226
59
0.199
1324
X-RAY DIFFRACTION
100
1.982-2.102
0.234
78
0.189
1239
X-RAY DIFFRACTION
100
2.102-2.247
0.219
69
0.181
1166
X-RAY DIFFRACTION
100
2.247-2.427
0.182
43
0.165
1112
X-RAY DIFFRACTION
100
2.427-2.658
0.199
49
0.153
1024
X-RAY DIFFRACTION
100
2.658-2.97
0.193
62
0.154
929
X-RAY DIFFRACTION
100
2.97-3.428
0.236
38
0.164
838
X-RAY DIFFRACTION
100
3.428-4.195
0.156
39
0.142
709
X-RAY DIFFRACTION
99.7333
4.195-5.915
0.213
38
0.168
558
X-RAY DIFFRACTION
99.4992
+
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