Resolution: 2.55→48.37 Å / SU ML: 0.3087 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.2155 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: For the most disordered regions, the modeled nucleotides were refined with occupancy = 0. The list of nucleotides is: chain A - G1, C2, G48, C49, chain B - G6, C44, C47, and C49.
Rfactor
Num. reflection
% reflection
Rfree
0.21
908
9.59 %
Rwork
0.183
8556
-
obs
0.1965
9499
98.72 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 81.95 Å2
Refinement step
Cycle: LAST / Resolution: 2.55→48.37 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
1952
45
49
2046
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.0064
2226
X-RAY DIFFRACTION
f_angle_d
1.196
3468
X-RAY DIFFRACTION
f_chiral_restr
0.0597
448
X-RAY DIFFRACTION
f_plane_restr
0.0074
96
X-RAY DIFFRACTION
f_dihedral_angle_d
20.428
1072
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.55-2.71
0.2813
124
0.2297
1442
X-RAY DIFFRACTION
98.06
2.71-2.92
0.3216
137
0.28
1407
X-RAY DIFFRACTION
99.29
2.92-3.21
0.2623
163
0.2073
1419
X-RAY DIFFRACTION
99.18
3.21-3.68
0.2377
151
0.2026
1431
X-RAY DIFFRACTION
98.32
3.68-4.63
0.1679
166
0.1621
1397
X-RAY DIFFRACTION
98.8
4.63-48.37
0.193
167
0.1764
1460
X-RAY DIFFRACTION
98.73
Refinement TLS params.
Method: refined / Origin x: 5.02849723171 Å / Origin y: -6.77033324989 Å / Origin z: 3.71842876319 Å
11
12
13
21
22
23
31
32
33
T
0.171454659106 Å2
0.01914279035 Å2
-0.0236877741146 Å2
-
0.0953612776025 Å2
-0.0476647394325 Å2
-
-
0.554355114973 Å2
L
3.4256728706 °2
0.10235291996 °2
0.305756618098 °2
-
2.71498053952 °2
-0.976017850471 °2
-
-
1.35220920525 °2
S
0.07406911406 Å °
-0.0536912306919 Å °
-0.135250564601 Å °
0.0430864329761 Å °
0.0105285273919 Å °
-0.121509858304 Å °
0.0189669361176 Å °
0.00383248181266 Å °
-0.0802579135404 Å °
Refinement TLS group
Selection details: all
+
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