X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.7
Details PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION USING THE SITTING-DROP METHOD. THE DROP CONTAINED 5-7 MG/ML PROTEIN, 20 MM TRIS/CL AT PH 7.7, 100MM LICL, 20MM MGSO4, 1.2% BETA-D-OCTYLGLUCOPYRANOSIDE AND 6-9% PEG-2000. THE CONCENTRATION OF PEG IN THE RESERVOIR WAS 12-15%. 2M SUCROSE WAS ADDED TO THE DROP FOR COCRYSTALLIZATION., vapor diffusion - sitting drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.8 α = 90
b = 111.8 β = 90
c = 147.8 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 287
Diffraction Detector
Detector Diffraction Type Details Collection Date
DIFFRACTOMETER STOE COLLIMATOR 1995-04
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
-- SCHNEIDER -- -- --

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
2.4 17 80.7 -- 0.155 -- 2.74 -- 65815 -- 0.0 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)
2.4 3.0 84.0 -- 0.524 2.0 2.6 --

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
DIFFERENCE FOURIER 2.4 100.0 -- 1.0 -- 55335 891 67.4 -- 0.207 0.207 0.246 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 2.4 2.49 -- 41 4826 0.2945 0.3694 0.058 59.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.4
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.11
x_scbond_it 2.11
x_mcangle_it 2.6
x_mcbond_it 1.52
x_improper_angle_d 1.39
x_bond_d 0.011
x_angle_deg 1.73
x_dihedral_angle_d 28.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.37
Luzzati Resolution Cutoff (Low) 17.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.43
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9606
Nucleic Acid Atoms 0
Heterogen Atoms 141
Solvent Atoms 330

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
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