X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9.5
Temperature 298.0
Details PEG 8000 12%, NaCl 0.2 M, CHESS 0.1 M, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.73 α = 90
b = 91.73 β = 90
c = 89.58 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2000-11-10
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X9B 0.98 NSLS X9B

Data Collection

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)
3.0 50.0 94.9 0.15 0.061 0.24 5.8 4739

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 3.0 29.72 2.0 0.0 5162 5162 291 91.9 -- -- 0.333 0.308 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 3.0 3.19 -- 37 615 0.566 0.646 0.106 68.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 73.7
Anisotropic B[1][1] 7.75
Anisotropic B[1][2] 14.47
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -15.51
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 24.1
c_scbond_it 3.08
c_bond_d 0.011
c_mcangle_it 15.51
c_scangle_it 3.64
c_angle_deg 1.9
c_improper_angle_d 1.15
c_mcbond_it 12.54
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.66
Luzzati Sigma A (Observed) 1.09
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.49
Luzzati Sigma A (R-Free Set) 1.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1920
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALA data scaling
CNS refinement
CCP4 data scaling version: (SCALA)
CNS phasing