Resolution: 2.7→47.79 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.782 / SU ML: 0.266 / Cross valid method: FREE R-VALUE / ESU R Free: 0.354 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2532
586
4.924 %
Rwork
0.1936
11316
-
all
0.196
-
-
obs
-
11902
99.933 %
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: 45.168 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.848 Å2
-0 Å2
0 Å2
2-
-
0.639 Å2
-0 Å2
3-
-
-
0.209 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→47.79 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2848
0
15
73
2936
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.012
2934
X-RAY DIFFRACTION
r_ext_dist_refined_d
0.278
0.1
40689
X-RAY DIFFRACTION
r_angle_refined_deg
1.744
1.648
3969
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
10.113
5
356
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.42
22.405
158
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.975
15
509
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.966
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.126
0.2
364
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
2250
X-RAY DIFFRACTION
r_nbd_refined
0.222
0.2
1233
X-RAY DIFFRACTION
r_nbtor_refined
0.314
0.2
1965
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.147
0.2
96
X-RAY DIFFRACTION
r_metal_ion_refined
0.141
0.2
3
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.208
0.2
51
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.286
0.2
7
X-RAY DIFFRACTION
r_mcbond_it
3.456
4.29
1433
X-RAY DIFFRACTION
r_mcangle_it
5.638
6.422
1785
X-RAY DIFFRACTION
r_scbond_it
4.378
4.716
1500
X-RAY DIFFRACTION
r_scangle_it
6.841
6.895
2183
X-RAY DIFFRACTION
r_lrange_it
10.929
152.156
41236
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.7-2.77
0.352
31
0.321
836
X-RAY DIFFRACTION
100
2.77-2.846
0.379
39
0.295
803
X-RAY DIFFRACTION
99.763
2.846-2.929
0.353
18
0.267
816
X-RAY DIFFRACTION
100
2.929-3.019
0.26
35
0.255
748
X-RAY DIFFRACTION
100
3.019-3.118
0.313
39
0.249
729
X-RAY DIFFRACTION
100
3.118-3.227
0.289
43
0.218
734
X-RAY DIFFRACTION
99.8715
3.227-3.349
0.219
37
0.216
663
X-RAY DIFFRACTION
100
3.349-3.485
0.254
58
0.199
644
X-RAY DIFFRACTION
100
3.485-3.64
0.281
45
0.192
638
X-RAY DIFFRACTION
100
3.64-3.818
0.208
49
0.166
576
X-RAY DIFFRACTION
100
3.818-4.024
0.293
32
0.164
585
X-RAY DIFFRACTION
100
4.024-4.268
0.191
31
0.142
561
X-RAY DIFFRACTION
100
4.268-4.563
0.207
15
0.123
528
X-RAY DIFFRACTION
100
4.563-4.928
0.147
15
0.128
497
X-RAY DIFFRACTION
100
4.928-5.397
0.178
24
0.154
459
X-RAY DIFFRACTION
100
5.397-6.033
0.166
15
0.18
411
X-RAY DIFFRACTION
100
6.033-6.965
0.315
17
0.202
367
X-RAY DIFFRACTION
99.7403
6.965-8.525
0.22
27
0.2
317
X-RAY DIFFRACTION
100
8.525-12.034
0.436
12
0.185
249
X-RAY DIFFRACTION
100
12.034-47.79
0.758
4
0.283
155
X-RAY DIFFRACTION
97.546
+
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