X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 289.0
Details 1.3-1.4 M ammonium sulfate, 8 % glycerol, 100 mM glycine-NaOH pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.5 α = 90
b = 116.5 β = 90
c = 69.8 γ = 90
Symmetry
Space Group I 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD BRANDEIS -- --
IMAGE PLATE RIGAKU RAXIS IV -- --
Diffraction Radiation
Monochromator Protocol
-- Two wavelengths
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C 0.95189, 0.950051 NSLS X12C
ROTATING ANODE RIGAKU 200 1.54 -- --
SYNCHROTRON NSLS BEAMLINE X12C 0.98 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
1.8 20 96.8 0.051 -- -- 3.5 41963 146987 -- 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 1.83 93.2 0.206 -- 3.74 -- 1976

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
MIR 1.8 20.0 -- 0.0 37121 -- 1883 -- -- -- 0.21 0.25 5% of total reflection (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 1.8 20.0 37121 1883 -- 0.21 0.25 -- 86.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 0.943
RMS Deviations
Key Refinement Restraint Deviation
x_bond_d 0.01
x_angle_d 1.5
x_dihedral_angle_d 23.4
x_improper_angle_d 1.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2474
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 256

Software

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