X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 6.7
Temperature 287.0
Details BES, EDTA, 10mM N-benzoyl-N'-beta-D-glucopyranosyl urea, pH 6.7, SMALL TUBES, temperature 287K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.52 α = 90
b = 128.52 β = 90
c = 116.5 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors 2001-04-02
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.26 28.75 95.8 -- 9.6 -- 5.3 44261 44361 0.0 -3.0 28.0
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)
2.26 2.3 86.5 -- 42.4 2.6 4.2 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
FOURIER SYNTHESIS 2.26 28.75 -- 0.0 44199 44199 2247 95.8 -- -- 0.18 0.212 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 2.26 2.4 -- 371 6525 0.304 0.336 0.017 91.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 33.5
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
x_mcbond_it 2.02
x_scbond_it 3.65
x_bond_d 0.007
x_dihedral_angle_d 25.1
x_improper_angle_d 0.72
x_scangle_it 5.65
x_angle_deg 1.3
x_mcangle_it 3.21
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.32
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6643
Nucleic Acid Atoms 0
Heterogen Atoms 61
Solvent Atoms 249

Software

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