X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.6
Details PROTEIN WAS CRYSTALLIZED FROM 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 5.6; THEN CROSS-LINKED WITH 10% GLUTARALDEHYDE IN 13% SODIUM SULFATE, 30 MM CACODYLATE, PH 7.5, WASHED WITH DISTILLED WATER, AND TRANSFERRED TO 20% DIOXANE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.56 α = 90
b = 55.17 β = 90
c = 53.86 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 296
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II MIRRORS 1998-01-17
Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
2.2 20 93.8 -- 0.129 -- 3.9 -- 11408 -- -- 27.0
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)
2.2 2.3 85.0 -- 0.36 3.9 2.9 --

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
MOLECULAR REPLACEMENT 2.2 20.0 -- 2.0 -- 11000 -- -- -- 0.187 0.187 0.245 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 2.2 -- -- 1031 0.262 0.338 -- 85.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.0
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 0.689
x_bond_d 0.007
x_angle_deg 1.2
x_dihedral_angle_d 26.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.28
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1920
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 90

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.8 Structure Solution
X-PLOR 3.8 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.8 refinement
X-PLOR version: 3.8 model building