Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→46.389 Å / SU ML: 0.43 / σ(F): 0 / Phase error: 29.6 / Stereochemistry target values: ML Details: I/SIGMAS WERE EXTREMELY LOW FOR THE HIGH RESOLUTION REFLECTIONS, AS WAS THE COMPLETENESS. THE AUTHORS TRUNCATED THE DATA USED IN REFINEMENT TO ONLY INCLUDE DATA WITH HIGH ENOUGH INTENSITY AND COMPLETENESS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.3107
348
4.85 %
Random
Rwork
0.252
-
-
-
all
0.2548
7265
-
-
obs
0.2548
7176
98.77 %
-
Solvent computation
Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.921 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
5.8595 Å2
0 Å2
-0 Å2
2-
-
5.8595 Å2
-0 Å2
3-
-
-
-11.719 Å2
Refinement step
Cycle: LAST / Resolution: 3→46.389 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2370
0
19
0
2389
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.01
2449
X-RAY DIFFRACTION
f_angle_d
0.959
3325
X-RAY DIFFRACTION
f_dihedral_angle_d
15.197
883
X-RAY DIFFRACTION
f_chiral_restr
0.057
368
X-RAY DIFFRACTION
f_plane_restr
0.005
427
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3-3.7798
0.3741
181
0.2999
3293
X-RAY DIFFRACTION
99
3.7798-46.389
0.2752
167
0.2283
3535
X-RAY DIFFRACTION
98
+
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