Resolution: 1.53→37.621 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.279 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.086 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2254
756
5.197 %
Rwork
0.1913
13791
-
all
0.193
-
-
obs
-
14547
98.151 %
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: 16.202 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.001 Å2
-0.001 Å2
-0 Å2
2-
-
-0.001 Å2
0 Å2
3-
-
-
0.005 Å2
Refinement step
Cycle: LAST / Resolution: 1.53→37.621 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
378
332
101
811
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.025
0.018
792
X-RAY DIFFRACTION
r_bond_other_d
0.033
0.025
346
X-RAY DIFFRACTION
r_angle_refined_deg
3.091
2.131
1208
X-RAY DIFFRACTION
r_angle_other_deg
3.85
3.211
818
X-RAY DIFFRACTION
r_chiral_restr
0.505
0.2
142
X-RAY DIFFRACTION
r_chiral_restr_other
1.751
0.2
22
X-RAY DIFFRACTION
r_gen_planes_refined
0.023
0.021
400
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.023
148
X-RAY DIFFRACTION
r_nbd_refined
0.156
0.2
75
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.212
0.2
478
X-RAY DIFFRACTION
r_nbtor_refined
0.252
0.2
295
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.3
0.2
154
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.206
0.2
53
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.176
0.2
15
X-RAY DIFFRACTION
r_nbd_other
0.247
0.2
63
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.258
0.2
21
X-RAY DIFFRACTION
r_scbond_it
2.141
1.606
792
X-RAY DIFFRACTION
r_scbond_other
2.044
1.583
785
X-RAY DIFFRACTION
r_scangle_it
3.16
2.43
1208
X-RAY DIFFRACTION
r_scangle_other
3.05
2.393
1197
X-RAY DIFFRACTION
r_lrange_it
4.882
15.478
1063
X-RAY DIFFRACTION
r_lrange_other
4.804
15.126
1049
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.532-1.572
0.278
49
0.21
963
X-RAY DIFFRACTION
95.3817
1.572-1.615
0.2
54
0.192
1001
X-RAY DIFFRACTION
99.3409
1.615-1.662
0.247
63
0.17
934
X-RAY DIFFRACTION
99.6004
1.662-1.713
0.155
46
937
X-RAY DIFFRACTION
98.794
1.713-1.769
0.234
48
0.167
891
X-RAY DIFFRACTION
98.9463
1.769-1.831
0.197
31
0.166
898
X-RAY DIFFRACTION
99.3583
1.831-1.9
0.213
64
0.181
820
X-RAY DIFFRACTION
97.6796
1.9-1.978
0.22
58
0.175
822
X-RAY DIFFRACTION
99.0991
1.978-2.066
0.169
39
779
X-RAY DIFFRACTION
99.6346
2.066-2.166
0.271
50
0.182
741
X-RAY DIFFRACTION
98.3831
2.166-2.283
0.194
31
0.187
721
X-RAY DIFFRACTION
98.1723
2.283-2.422
0.26
27
0.221
677
X-RAY DIFFRACTION
97.7778
2.422-2.589
0.3
35
0.21
634
X-RAY DIFFRACTION
98.0938
2.589-2.796
0.301
37
0.233
587
X-RAY DIFFRACTION
97.1963
2.796-3.063
0.241
31
0.206
549
X-RAY DIFFRACTION
97.973
3.063-3.424
0.252
25
0.203
486
X-RAY DIFFRACTION
94.2804
3.424-3.952
0.165
33
448
X-RAY DIFFRACTION
97.5659
3.952-4.838
0.246
11
0.173
386
X-RAY DIFFRACTION
95.6627
4.838-6.831
0.14
16
315
X-RAY DIFFRACTION
99.6988
6.831-37.621
0.535
8
0.296
202
X-RAY DIFFRACTION
97.2222
+
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