1JH8

Structural Investigation of the Biosynthesis of Alternative Lower Ligands for Cobamides by Nicotinate Mononucleotide:5,6-Dimethylbenzimidazole Phosphoribosyltransferase (CobT) from Salmonella enterica


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 1.4 M Ammonium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.6 α = 90
b = 90 β = 90
c = 47.6 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 278
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR SIEMENS HI-STAR -- 1999-10-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.8 30 86.6 0.042 -- -- 2.9 -- 25292 0.0 -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.8 1.85 64.4 0.141 -- 2.7 1.3 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
FOURIER SYNTHESIS 1.8 30.0 -- 0.0 -- 25292 2529 -- -- -- 0.175 0.256 random
RMS Deviations
Key Refinement Restraint Deviation
t_bond_d 0.01
t_angle_deg 1.92
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2436
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 116

Software

Software
Software Name Purpose
XDS data reduction
TNT refinement
XDS data scaling
TNT phasing