X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 1.6M Ammonium Sulfate, 2% PEG 1000, 0.1M sodium HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 151.73 α = 90
b = 151.73 β = 90
c = 79.46 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 16 pole wiggler 2002-01-30
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.98 SSRL BL9-2

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
2.3 30 97.7 0.064 0.064 -- 4.94 45896 45896 0.0 -3.0 20.8
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)
2.3 2.35 97.2 0.265 0.265 3.0 -- 3012

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 REPLACEMENT 2.3 30.0 0.0 0.0 45879 45879 2190 97.6 0.186 0.183 0.183 0.232 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 2.3 2.44 -- 351 7162 0.224 0.298 0.016 96.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.3
Anisotropic B[1][1] 1.64
Anisotropic B[1][2] 6.81
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.28
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.17
c_dihedral_angle_d 25.0
c_angle_deg 1.8
c_bond_d 0.017
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.32
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6083
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 318

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection