Resolution: 1.91→46.613 Å / Num. obs: 47228 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 31.75 Å2 / Rsym value: 0.082 / Net I/σ(I): 13.3
Reflection shell
Resolution: 2.25→2.31 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.356 / % possible all: 99.7
-
Processing
Software
Name
Version
Classification
Blu-Ice
datacollection
MOSFLM
datareduction
SCALA
datascaling
CCP4
datareduction
SnB
phasing
MLPHARE
phasing
CCP4
modelbuilding
SOLVE
phasing
CNS
refinement
CCP4
(SCALA)
datascaling
RESOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.9→46.61 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: THERE IS A SIGNIFICANT PIECE OF DENSITY THAT HAS NOT BEEN ACCOUNTED FOR IN THE MODEL THAT IS LOCATED IN THE PUTATIVE ACTIVE SITE. IT IS "SANDWICHED" BETWEEN HIS 57 AND MSE 60. IT IS ALSO ...Details: THERE IS A SIGNIFICANT PIECE OF DENSITY THAT HAS NOT BEEN ACCOUNTED FOR IN THE MODEL THAT IS LOCATED IN THE PUTATIVE ACTIVE SITE. IT IS "SANDWICHED" BETWEEN HIS 57 AND MSE 60. IT IS ALSO WITHIN INTER-ACTION DISTANCE OF A WATER (HOH 14) THAT IS COORDINATED TO THE ACTIVE SITE METAL ION. IT IS NOT YET POSSIBLE TO ASSIGN THE IDENTITY OF THIS/THESE MOLECULES AS THE STRUCTURE IS OF A PROTEIN OF UNKNOWN FUNCTION. FURTHER BIOCHEMICAL CHARACTERIZATION OF TM0936 MAY AID IN ELUCIDATING THE NATURE OF THIS DENSITY. THE MODEL SEQUENCE MATCHES THE DATABASE SEQUENCE WITH THE FOLLOWING EXCEPTIONS: RESIDUES -1 AND 0 ARE HIS 5 AND 6 OF THE 6-HIS PURIFICATION TAG. THERE IS NO DENSITY FOR SER406 AND THIS DOES NOT APPEAR IN THE MODEL. PROCHECK IDENTIFIES 3 RESIDUES IN DISFAVORED CONFORMATIONS. HIS 228 (DISALLOWED REGION), ASP 279 AND ASN 285 (GENEROUSLY ALLOWED REGION). HIS 228 AND ASP 279 COORDINATE THE PUTATIVE ACTIVE SITE METAL ION. THE BINDING OF THE ACTIVE SITE METAL ION APPEARS TO INDUCE THESE OTHERWISE UNFAVORABLE GEOMETRIES. ASN 285 IS ON THE PROTEIN SURFACE AT A CRYSTALLOGRAPHIC INTERFACE. PROCHECK ADDITIONALLY IDENTIFIES 1 CIS-PEPTIDE RESIDUE PRO 352 WHICH DOES NOT APPEAR TO BE INVOLVED IN THE ACTIVE SITE. A METAL ION IDENTIFIED AS NICKEL BY FLUORESCENCE SCAN IS COORDINATED IN THE PUTATIVE ACTIVE SITE. AS WITH THE UNIDENTIFIED DENSITY PREVIOUSLY NOTED, IT IS NOT POSSIBLE TO DETERMINE IF THE NICKEL ION IS AN ARTIFACT OF NICKEL-CHELATING PURIFICATION OF TM0936 OR THE NATIVE METAL REQUIRED FOR ACTIVITY AS TM0936 IS A PROTEIN OF UNKNOWN FUNCTION. FURTHER BIOCHEMICAL CHARACTERIZATION OF TM0936 MAY AID IN ELUCIDATING THE NATURE OF THIS METAL ION.
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