X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 1.6 M LiSO4, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.78 α = 90
b = 89.78 β = 90
c = 108.95 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-11-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.000000 APS 14-BM-C

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 30 98.1 0.073 -- -- 12.0 253617 17892 16525.0 486.0 23.7
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 30.0 98.1 0.337 -- 7.0 10.0 1710

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
isomorphous to native 2.0 14.96 -- -- 253617 17249 1699 95.5 -- 0.237 0.237 0.286 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 2.12 -- 263 2460 0.287 0.314 0.019 93.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 37.4
Anisotropic B[1][1] 1.16
Anisotropic B[1][2] 3.59
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.33
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.01
c_mcbond_it 1.13
c_scbond_it 1.9
c_mcangle_it 1.83
c_angle_deg 1.4
c_dihedral_angle_d 22.1
c_scangle_it 2.75
c_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.23
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.24
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1274
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 70

Software

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