Resolution: 1.93→19.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.268 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.173 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2287
602
5.215 %
Rwork
0.1841
10942
-
all
0.186
-
-
obs
-
11544
99.116 %
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: 34.064 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.518 Å2
-0 Å2
-0 Å2
2-
-
-0.861 Å2
0 Å2
3-
-
-
0.342 Å2
Refinement step
Cycle: LAST / Resolution: 1.93→19.81 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1492
0
0
116
1608
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.013
1540
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
1382
X-RAY DIFFRACTION
r_angle_refined_deg
1.536
1.64
2100
X-RAY DIFFRACTION
r_angle_other_deg
1.343
1.57
3230
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.506
5
191
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.785
25.342
73
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.143
15
258
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.156
15
2
X-RAY DIFFRACTION
r_chiral_restr
0.081
0.2
204
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
1706
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
304
X-RAY DIFFRACTION
r_nbd_refined
0.2
0.2
286
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.172
0.2
1295
X-RAY DIFFRACTION
r_nbtor_refined
0.167
0.2
743
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.079
0.2
671
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.211
0.2
83
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_other
0.081
0.2
1
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.262
0.2
50
X-RAY DIFFRACTION
r_nbd_other
0.222
0.2
102
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.228
0.2
22
X-RAY DIFFRACTION
r_mcbond_it
2.819
3.376
752
X-RAY DIFFRACTION
r_mcbond_other
2.796
3.373
751
X-RAY DIFFRACTION
r_mcangle_it
3.885
5.042
938
X-RAY DIFFRACTION
r_mcangle_other
3.885
5.044
939
X-RAY DIFFRACTION
r_scbond_it
4.108
3.823
788
X-RAY DIFFRACTION
r_scbond_other
4.098
3.818
786
X-RAY DIFFRACTION
r_scangle_it
5.932
5.573
1159
X-RAY DIFFRACTION
r_scangle_other
5.935
5.573
1159
X-RAY DIFFRACTION
r_lrange_it
7.561
39.937
1697
X-RAY DIFFRACTION
r_lrange_other
7.563
39.726
1679
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.158
0.05
2610
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.93-1.98
0.27
34
0.25
732
X-RAY DIFFRACTION
91.082
1.98-2.034
0.227
48
0.219
773
X-RAY DIFFRACTION
99.8783
2.034-2.093
0.287
40
0.217
760
X-RAY DIFFRACTION
100
2.093-2.157
0.254
51
0.196
719
X-RAY DIFFRACTION
100
2.157-2.228
0.182
27
0.204
734
X-RAY DIFFRACTION
100
2.228-2.306
0.287
35
0.192
685
X-RAY DIFFRACTION
100
2.306-2.392
0.219
42
0.198
681
X-RAY DIFFRACTION
100
2.392-2.49
0.314
25
0.201
640
X-RAY DIFFRACTION
100
2.49-2.6
0.258
40
0.201
625
X-RAY DIFFRACTION
99.8499
2.6-2.726
0.275
23
0.208
607
X-RAY DIFFRACTION
100
2.726-2.873
0.282
35
0.188
551
X-RAY DIFFRACTION
100
2.873-3.046
0.234
25
0.18
553
X-RAY DIFFRACTION
99.6552
3.046-3.255
0.216
29
0.185
506
X-RAY DIFFRACTION
100
3.255-3.514
0.221
35
0.166
472
X-RAY DIFFRACTION
99.6071
3.514-3.846
0.186
23
0.158
442
X-RAY DIFFRACTION
99.7854
3.846-4.294
0.191
34
0.156
383
X-RAY DIFFRACTION
99.2857
4.294-4.948
0.152
17
0.159
373
X-RAY DIFFRACTION
100
4.948-6.036
0.218
15
0.191
309
X-RAY DIFFRACTION
99.6923
6.036-8.434
0.198
14
0.183
251
X-RAY DIFFRACTION
100
8.434-19.81
0.355
10
0.204
146
X-RAY DIFFRACTION
90.1734
+
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