X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 310.0
Details sodium phosphate, potassium phosphate, 1,4-butandiol, HEPES, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.9 α = 90
b = 54.9 β = 90
c = 176.8 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Supper mirror 2000-08-04
Diffraction Radiation
Monochromator Protocol
Supper mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-5 1.54180 -- --

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
1.86 15 99.9 0.079 -- -- 10.0 25165 25142 0.0 -3.0 20.4
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)
1.86 1.91 98.1 0.752 -- 3.5 8.6 --

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 1.86 15.0 0.0 0.0 -- 25152 1241 99.8 0.2 0.2 0.198 0.22 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 1.86 1.98 4011 166 4011 0.258 0.288 0.022 99.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.1
Anisotropic B[1][1] 3.36
Anisotropic B[1][2] 2.61
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.73
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.2
c_scbond_it 1.95
c_dihedral_angle_d 25.6
c_mcbond_it 1.53
c_bond_d 0.005
c_improper_angle_d 0.7
c_mcangle_it 2.52
c_scangle_it 2.89
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.15
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.17
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2260
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 157

Software

Software
Software Name Purpose
CNS refinement
DENZO data reduction
SCALEPACK data scaling
CNS phasing