X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details PROTEIN WAS CRYSTALLIZED FROM 30% PEG-400, 100 MM HEPES PH 7.5, 0.2 M MGCL2. CRYSTAL WAS SOAKED IN 0.1 M SODIUM ACETATE, 30% PEG-400, 0.2 M MGCL2, PH 5.8 PRIOR TO DATA COLLECTION.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.12 α = 90
b = 57.12 β = 90
c = 80.24 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC MIRRORS 1995-05
Diffraction Radiation
Monochromator Protocol
NI --
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
1.95 45 92.0 -- -- -- -- -- 9031 -- 2.0 19.4
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)
1.94 1.97 65.7 -- -- -- -- --

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/MOLECULAR REPLACEMENT 1.95 45.0 -- 2.0 -- 9030 928 82.0 -- 0.195 0.195 0.287 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 1.9 2.02 -- 86 722 0.386 0.44 0.047 45.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 39.3
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 8.44
x_scbond_it 5.61
x_mcangle_it 4.94
x_mcbond_it 3.41
x_improper_angle_d 1.12
x_bond_d 0.016
x_angle_deg 1.9
x_dihedral_angle_d 25.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.41
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.47
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 878
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 96

Software

Computing
Computing Package Purpose
PROCESS Data Reduction (intensity integration)
PROCESS Data Reduction (data scaling)
EPMR, X-PLOR 3.851 Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR version: 3.851 model building
EPMR model building
PROCESS data reduction
PROCESS data collection