Journal: Appl.Microbiol.Biotechnol. / Year: 2015 Title: Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D- ...Title: Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate Authors: Matsumoto, Y. / Yasutake, Y. / Takeda, Y. / Tamura, T. / Yokota, A. / Wada, M.
Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.98 Å / Relative weight: 1
Reflection
Resolution: 1.5→50 Å / Num. all: 157557 / Num. obs: 157557 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 33.66
Reflection shell
Resolution: 1.5→1.53 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 4.99 / Num. unique all: 7806 / % possible all: 100
-
Processing
Software
Name
Version
Classification
ADSC
Quantum
datacollection
SHELXCD
phasing
SHELXE
modelbuilding
REFMAC
5.6.0117
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.5→45.63 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.585 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1518
7908
5 %
RANDOM
Rwork
0.1211
-
-
-
obs
0.1227
149594
99.88 %
-
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