X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 293.0
Details PEG-4000, cadmium chloride, coenzyme B12, sodium glutamate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.35 α = 90
b = 113.14 β = 96
c = 108.44 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 103
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-08-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, Hamburg BW7B

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
1.9 30 99.9 0.073 0.073 -- 4.6 121680 121680 0.0 0.0 15.5
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)
1.9 1.94 100.0 0.281 0.281 5.0 3.7 8102

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
RIGID BODY REFINEMENT 1.9 30.0 0.0 0.0 121680 121680 6137 99.9 0.1705 0.1705 0.168 0.221 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 13.3
RMS Deviations
Key Refinement Restraint Deviation
s_similar_adp_cmpnt 0.038
s_bond_d 0.008
s_approx_iso_adps 0.0
s_similar_dist 0.032
s_anti_bump_dis_restr 0.016
s_non_zero_chiral_vol 0.048
s_angle_d 0.025
s_zero_chiral_vol 0.045
s_from_restr_planes 0.34
s_rigid_bond_adp_cmpnt 0.0
Coordinate Error
Parameter Value
Number Disordered Residues 39.0
Occupancy Sum Hydrogen 9804.0
Occupancy Sum Non Hydrogen 11102.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9606
Nucleic Acid Atoms 0
Heterogen Atoms 258
Solvent Atoms 1258

Software

Software
Software Name Purpose
REFMAC refinement
SHELXL-97 refinement
DENZO data reduction
SCALEPACK data scaling