X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 296.0
Details potassium phosphate, MgCl2, ammonium sulfate, DTT, EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.6 α = 90
b = 127.6 β = 90
c = 68 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 296
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- 1997-03-17
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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
2.2 40 95.0 0.088 -- -- 4.0 30601 30601 0.0 -3.0 15.7
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)
2.2 2.3 84.0 0.342 -- 3.2 -- --

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
FOURIER SYNTHESIS 2.2 32.5 -- 0.0 30499 30499 3060 94.7 -- 0.202 0.198 0.241 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 2.2 2.34 -- 494 4159 0.34 0.366 0.016 87.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 36.8
Anisotropic B[1][1] -1.62
Anisotropic B[1][2] 1.04
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.62
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.23
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 24.1
c_bond_d 0.007
c_angle_deg 1.6
c_improper_angle_d 0.88
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.41
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.47
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4306
Nucleic Acid Atoms 0
Heterogen Atoms 138
Solvent Atoms 196

Software

Software
Software Name Purpose
X-PLOR model building
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing