X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.25
Temperature 294.0
Details 2,4-methylpentanediol, sodium acetate, calcium chloride, pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.54 α = 90
b = 122.24 β = 90
c = 180.03 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-06-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2

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
2.3 30 97.0 0.034 -- -- 3.3 54160 51997 -3.0 -3.0 47.0
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)
2.3 2.35 97.7 0.275 -- 3.8 2.9 3473

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 2.3 5.0 -- 0.0 51364 51364 2620 97.0 -- -- 0.239 0.29 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 2.3 2.38 -- 225 -- -- -- -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model No B value correction in scaling Fcalc to Fobs during refinement. Final R calculation with K=1.2137 B=0.44240 (TNT)
Mean Isotropic B 57.0
RMS Deviations
Key Refinement Restraint Deviation
t_bond_d 0.006
t_angle_deg 1.174
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.56
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5069
Nucleic Acid Atoms 1347
Heterogen Atoms 0
Solvent Atoms 283

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
TNT refinement
TNT phasing