Resolution: 2.5→2.59 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 3.65 / Num. unique all: 933 / % possible all: 97.9
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SHELX
D/E
modelbuilding
RESOLVE
modelbuilding
PHENIX
(phenix.refine: 1.5_2)
refinement
DENZO
datareduction
SCALEPACK
datascaling
SHELX
D/E
phasing
RESOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.494→27.538 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.27 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.248
426
4.61 %
RANDOM
Rwork
0.2131
-
-
-
obs
0.2147
9232
99.5 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.652 Å2 / ksol: 0.289 e/Å3
Refinement step
Cycle: LAST / Resolution: 2.494→27.538 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
985
0
0
14
999
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
1006
X-RAY DIFFRACTION
f_angle_d
1.639
1357
X-RAY DIFFRACTION
f_dihedral_angle_d
21.267
374
X-RAY DIFFRACTION
f_chiral_restr
0.112
143
X-RAY DIFFRACTION
f_plane_restr
0.009
178
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.4944-2.855
0.3652
141
0.2851
2955
X-RAY DIFFRACTION
99
2.855-3.5958
0.3074
152
0.2322
2912
X-RAY DIFFRACTION
100
3.5958-27.5397
0.1996
133
0.1852
2939
X-RAY DIFFRACTION
99
+
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