X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 296.0
Details sodium sulfate, sodium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.7 α = 90
b = 63.14 β = 90
c = 69.47 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 291
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2003-02-04
Diffraction Radiation
Monochromator Protocol
GRAPHITE 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 37.7 95.6 0.0796 -- -- 3.5 19424 18579 4.0 2.0 20.6
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)
2.0 2.11 89.0 0.2698 -- 3.3 3.5 2839

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 2.0 20.31 -- 0.0 18575 18575 739 95.2 0.165 0.162 0.162 0.185 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 2.0 2.07 -- 61 1624 0.245 0.264 0.034 88.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.3
Anisotropic B[1][1] -0.24
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.33
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.09
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.25
c_scbond_it 2.28
c_mcangle_it 2.04
c_mcbond_it 1.37
c_improper_angle_d 0.89
c_dihedral_angle_d 25.9
c_angle_deg 1.6
c_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1702
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 141

Software

Computing
Computing Package Purpose
R-AXIS Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement