X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details PEG 8000, sodium chloride, Hepes buffer, sodium azides, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.85 α = 90
b = 135.85 β = 90
c = 82.63 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- 1995-09-04
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
2.6 39.16 97.3 -- 0.074 -- 8.5 -- 26125 -- -- 43.4
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)
2.6 2.66 59.9 -- 0.34 -- 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
MOLECULAR REPLACEMEN 2.6 39.16 -- -- -- 26125 1782 97.3 -- 0.173 0.173 0.202 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 2.6 2.66 -- 74 996 0.237 0.316 0.037 59.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model GROUP
Mean Isotropic B 38.2
Anisotropic B[1][1] 3.31
Anisotropic B[1][2] 4.8
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.31
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.61
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 4.219
c_dihedral_angle_d 26.6
c_improper_angle_d 0.82
c_scbond_it 8.435
c_scangle_it 11.998
c_bond_d 0.006
c_mcangle_it 6.541
c_angle_deg 1.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.31
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.38
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3708
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 202

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MERLOT phasing
BRUTE model building
AMoRE phasing
CNS refinement
BRUTE phasing