- PDB-5u9c: 1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamno... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5u9c
Title
1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from Yersinia enterocolitica
Components
dTDP-4-dehydrorhamnose Reductase
Keywords
HYDROLASE / OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / dTDP-4-dehydrorhamnose Reductase
Function / homology
Function and homology information
dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process Similarity search - Function
Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2014 / Details: C(111)
Radiation
Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97872 Å / Relative weight: 1
Reflection
Resolution: 1.9→30 Å / Num. obs: 179762 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 28.8
Reflection shell
Resolution: 1.9→1.93 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.887 / % possible all: 96.3
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0158
refinement
HKL-3000
datareduction
HKL-3000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.9→29.94 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 7.005 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19066
8981
5 %
RANDOM
Rwork
0.15993
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obs
0.16146
169660
99.57 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å