X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details (NH4)2SO4, ethanol, MgCl2, Hepes pH 7.0, farnesyl diphosphate, VAPOR DIFFUSION, SITTING DROP at 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 181.4 α = 90
b = 181.4 β = 90
c = 56.4 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC mirrors 2000-04-04
Diffraction Radiation
Monochromator Protocol
Yale mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200HB 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
2.9 20 96.8 0.083 0.083 -- 2.76 23110 23110 0.0 0.0 45.22
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)
2.9 3.0 95.8 0.404 0.404 2.5 1.0 2022

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 2.9 20.0 0.0 0.0 23827 22227 2195 93.3 0.2633 0.2633 0.2633 0.308 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 2.9 3.0 1828 197 -- 0.3961 0.4386 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Anisotropic B[1][1] -4.745
Anisotropic B[1][2] -9.118
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.745
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 9.49
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.83
c_dihedral_angle_d 18.88
c_angle_deg 1.3
c_bond_d 0.0085
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.47
Luzzati Sigma A (Observed) 0.64
Luzzati Resolution Cutoff (Low) 20.0
Luzzati ESD (R-Free Set) 0.54
Luzzati Sigma A (R-Free Set) 0.72
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4710
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 26

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
CNS model building
SCALEPACK data reduction
DENZO data collection