X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.05
Temperature 295.0
Details PEG2000 monomethyl ether, propanol, sodium azide, Hepes buffer, magnesium chloride, thiamin diphosphate, pH 7.05, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.69 α = 90
b = 141.6 β = 102.4
c = 82.46 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS - B4 toroidal mirror 2000-01-27
Diffraction Radiation
Monochromator Protocol
curved silicon monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 1.072 NSLS X12C

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
1.85 30 92.1 0.054 0.054 -- 3.6 146183 146183 0.0 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)
1.85 1.94 70.2 0.175 0.175 3.9 2.23 13132

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
MAD 1.85 8.0 1.0 2.0 144190 133768 8098 85.4 0.198 0.192 0.189 0.236 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.85 1.93 11667 674 10993 0.2361 0.2607 -- 62.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 17.5
RMS Deviations
Key Refinement Restraint Deviation
x_dihedral_angle_d 24.92
x_improper_angle_d 0.709
x_mcangle_it 2.1
x_scangle_it 4.06
x_scbond_it 2.71
x_bond_d 0.006
x_angle_deg 1.273
x_mcbond_it 1.41
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12682
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 682

Software

Software
Software Name Purpose
PHASES phasing
X-PLOR refinement version: 3.851
DENZO data reduction
SCALEPACK data scaling