Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 3.76 Å3/Da / Density % sol: 67.32 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Mother liquor consists of 2.3 -2.7M ammonium sulfate and 0.1M sodium acetate. The protein stock solution is 10mg/mL and is mixed with a 1:1 dilution with the mother liquor. The ligand is ...Details: Mother liquor consists of 2.3 -2.7M ammonium sulfate and 0.1M sodium acetate. The protein stock solution is 10mg/mL and is mixed with a 1:1 dilution with the mother liquor. The ligand is added to the protein stock solution at concentrations of 200-500 micromolar., pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
-
Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Resolution: 2.8→76.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2688886.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: DB75 ligand is disordered. The A and B chains and D and E chains form two distinct dimers. The A and B dimer assumes the drug bound conformation. The D and E dimer assumes the apo conformation.
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