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 ANHYDROUS DIOXANE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77 α = 90
b = 55.2 β = 90
c = 53.85 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 COLLIMATOR 1996-03-07
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
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
2.6 14 96.0 -- 0.14 -- 5.5 -- 7111 -- 2.0 --
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)
2.6 2.7 96.0 -- 0.38 4.3 5.2 --

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 2.6 6.0 -- 2.0 -- 6307 -- -- -- 0.161 0.161 0.248 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 2.6 2.7 -- -- 690 0.19 0.294 0.036 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 13.6
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 1.07
x_scbond_it 1.39
x_mcangle_it 1.12
x_mcbond_it 1.48
x_improper_angle_d 2.15
x_bond_d 0.012
x_angle_deg 1.68
x_dihedral_angle_d 25.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1920
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 65

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building