X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 289.0
Details sodium acetate, cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.78 α = 90
b = 127.78 β = 90
c = 113.26 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- 2004-04-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 0.98 ALS 4.2.2

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 99.2 0.074 -- -- 6.04 46651 46290 -- -- --
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 2.38 96.1 0.504 -- 2.3 4.39 4614

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 -- -- 85203 85203 8155 92.8 -- -- 0.2367 0.2621 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 2.38 7406 666 -- 0.446 0.464 0.018 81.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ANISOTROPIC
Mean Isotropic B 62.1
Anisotropic B[1][1] 13.32
Anisotropic B[1][2] 12.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 12.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -25.38
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_deg 0.78
c_dihedral_angle_deg 22.4
c_angle_deg 1.3
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.66
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.62
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3708
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 137

Software

Computing
Computing Package Purpose
SOFTWARE AT ALS 4.2.2 Data Reduction (intensity integration)
D*TREK Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
CNS model building
d*trek data reduction
ALS version: 4.2.2 data collection