Method to determine structure: SAD / Resolution: 2.49→48.68 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.845 / SU B: 17.206 / SU ML: 0.214 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.629 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The N-terminal His-tag (-19 to -1) is not visible in the electron density except for His (0). The inactive apo protein (no substrate) is cluster-free. The N-terminal domain, which normally ...Details: The N-terminal His-tag (-19 to -1) is not visible in the electron density except for His (0). The inactive apo protein (no substrate) is cluster-free. The N-terminal domain, which normally contains the active site with a [4Fe-4S] cluster and a site for substrate-binding is largely disordered. Residues 34-89, 93-95, 106, 110-11, 181-199 and 226-230 are not visible in the electron density in chain a. in chain b residues 34-92, 106-107, 110-111, 155 and 181-230 are disordered and not visible in the electron density. In addition, side chains of residues 95, 97 and 98 in chain b are truncated because of missing electron density.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2908
2086
5 %
RANDOM
Rwork
0.2295
-
-
-
all
0.2325
39386
-
-
obs
0.2325
39386
100 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
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