X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.6
Temperature 293.0
Details 0.1M Ammonium dihydrogen phosphate, 0.1M Tris HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.48 α = 90
b = 116.48 β = 90
c = 149.39 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER Mirror 2005-12-14
Diffraction Radiation
Monochromator Protocol
Mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2

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
2.42 50 99.6 0.083 -- -- 13.97 72738 72738 0.0 0.0 25.2
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)
2.42 2.51 100.0 0.356 -- 7.1 14.39 --

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 2.5 40.0 0.0 0.0 67557 67557 6656 -- -- 0.193 0.193 0.23 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 2.5 2.66 -- 1035 9905 0.421 0.392 0.012 99.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.77
c_mcangle_it 1.89
c_bond_d 0.006
c_angle_deg 1.1
c_mcbond_it 1.16
c_dihedral_angle_d 20.9
c_scangle_it 2.94
c_scbond_it 2.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.66
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.67
Luzzati Sigma A (R-Free Set) 0.56
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5740
Nucleic Acid Atoms 0
Heterogen Atoms 106
Solvent Atoms 288

Software

Software
Software Name Purpose
CNS refinement version: 1.1
d*TREK data reduction
CrystalClear data scaling version: (MSC/RIGAKU)
MOLREP phasing