X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 296.16
Details potassium phosphate, MgCl2, DTT, EDTA, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.16K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.8 α = 90
b = 127.8 β = 90
c = 68.1 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 -- 1997-04-01
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
2.5 40 22012.0 0.109 -- -- 5.0 21792 21792 0.0 -3.0 10.9
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)
2.5 2.57 93.0 0.385 -- 2.4 -- --

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 2.5 36.89 0.0 0.0 21792 21792 2165 98.6 -- 0.185 0.181 0.219 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 2.5 2.66 -- 341 3126 0.279 0.331 0.018 95.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.3
Anisotropic B[1][1] -0.59
Anisotropic B[1][2] 1.12
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.59
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.17
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.008
c_improper_angle_d 1.2
c_angle_deg 1.5
c_dihedral_angle_d 25.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.4
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.48
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4306
Nucleic Acid Atoms 0
Heterogen Atoms 106
Solvent Atoms 102

Software

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