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 10 mg/ml protein, 0.5 M sodium chloride, 0.05 M Na-Hepes(pH7.5), 12.5% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.21 α = 90
b = 57.97 β = 90
c = 135.3 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II mirrors 1999-06-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 -- -- --

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
2.8 40 99.5 -- 0.103 -- 6.0 61806 10232 0.0 0.0 66.4
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)
2.8 2.9 99.8 -- 0.51 -- 3.97 999

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
-- 2.8 19.78 0.0 0.0 10211 9915 1024 97.0 0.216 -- 0.216 0.277 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 2.8 2.97 -- 159 1390 0.274 0.355 0.028 93.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained
Mean Isotropic B 50.9
Anisotropic B[1][1] -7.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.87
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.69
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.015
c_mcangle_it 3.86
c_bond_d 0.008
c_improper_angle_d 0.71
c_mcbond_it 2.27
c_scbond_it 3.53
c_dihedral_angle_d 18.9
c_scangle_it 5.49
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.36
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.57
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2555
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 69

Software

Software
Software Name Purpose
X-PLOR model building
CNS refinement version: 0.9
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing