Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
-
Details
Has ligand of interest
Y
Has protein modification
Y
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal grow
Temperature: 311 K / Method: vapor diffusion, sitting drop Details: Prior to crystallization, protein was incubated with myristic acid (5 mM final concentration of fatty acid) for several hours at 37 oC. Then, 0.2 ul of 100 mg/ml protein in 25 mM Tris (pH 7. ...Details: Prior to crystallization, protein was incubated with myristic acid (5 mM final concentration of fatty acid) for several hours at 37 oC. Then, 0.2 ul of 100 mg/ml protein in 25 mM Tris (pH 7.4) and 50 mM NaCl were mixed with 0.2 ul of the well condition (25% PEG 3350, 50 mM K2HPO4 at pH 7.0), the crystallization plate was incubated at 37oC for several days and, after growth of the first HSA crystals, the plate was transferred to RT. JMS-053 powder (~50 ug) was added to the crystallization drop containing crystals, and then incubated for 48 h before harvesting.
-
Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
Resolution: 2.2→46.01 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.906 / SU B: 15.997 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2469
2640
4.9 %
RANDOM
Rwork
0.1924
-
-
-
obs
0.195
51130
84.33 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 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