Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
-
Details
Nonpolymer details
ZN ION SITS RIGHT ON THE NCS 2-FOLD THAT DEFINES THE DIMER INTERFACE AND IS COORDINATED ...ZN ION SITS RIGHT ON THE NCS 2-FOLD THAT DEFINES THE DIMER INTERFACE AND IS COORDINATED TETRAHEDRALLY WITH 2 PAIRS OF SYMMETRY-RELATED CYS RESIDUES.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal grow
Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 4000, CACODYLATE, MAGNESIUM ACETATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2→50 Å / Num. obs: 63795 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.5
Reflection shell
Resolution: 2→2.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.587 / % possible all: 92.9
-
Processing
Software
Name
Version
Classification
X-PLOR
modelbuilding
CNS
0.9
refinement
DENZO
datareduction
SCALEPACK
datascaling
X-PLOR
phasing
Refinement
Resolution: 2→32.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2575244.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: RESIDUES 39 TO 66 OF MOLECULE A AND RESIDUES 39 TO 68 IN MOLECULE B ARE NOT VISIBLE IN THE ELECTRON DENSITY. RESIDUES 108-120 ARE DISORDERED, BUT THE TENTATIVE MODEL WAS INCLUDED IN THE REFINEMENT.
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