Resolution: 1.49→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: About CD1/CD2 (LEU A 90), OE1/OE2 (GLU A 218) and CG1/CG2 (VAL A 325), there are 3 possible positions for these atoms. There are two different conformations for each atom. For convenience, ...Details: About CD1/CD2 (LEU A 90), OE1/OE2 (GLU A 218) and CG1/CG2 (VAL A 325), there are 3 possible positions for these atoms. There are two different conformations for each atom. For convenience, the author assigned as a double conformation only one of the atoms.(CD2 of LEU 90, OE1 of GLU 218 and CG1 of VAL 325) Thus the occupancies of the alternate conformations are greater than 1.00 and there are chirality errors at these atoms. The chirality errors appear at CB (ILE A 105) and CG (BLEU A 365). About LEU 365, the author could see two conformations, but only the atom CG was obvious. The other atoms (respectively CD1 and CD2), if in an other conformation, would have been too close than the first conformation. The author only applied two conformations for the CG atom. About ILE 105, the author could see density for an other conformation only for a CG atom, but nothing for the CD1. The author assigned only 2 conformations for the CG2 atom. These are the reasons for the chirality errors.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.213
4011
-
RANDOM
Rwork
0.202
-
-
-
all
0.203
83517
-
-
obs
0.203
79480
97 %
-
Refinement step
Cycle: LAST / Resolution: 1.49→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2847
0
1
296
3144
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.017
X-RAY DIFFRACTION
c_angle_deg
1.633
+
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