X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.05 α = 90
b = 128.05 β = 90
c = 112.76 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2003-09-10
Diffraction Radiation
Monochromator Protocol
Osmic 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
2.35 30 98.6 0.082 -- -- 5.0 43388 43388 -- -- --
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)
2.35 2.43 96.2 0.557 -- 2.13 3.88 4210

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 2.35 30.0 -- -- 43126 43126 4354 96.3 -- -- 0.222 0.259 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 2.35 2.43 4195 428 -- 0.32 0.35 -- 96.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Anisotropic
Mean Isotropic B 45.9
Anisotropic B[1][1] 5.79
Anisotropic B[1][2] 4.45
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -11.58
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.3
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.38
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.42
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3707
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 263

Software

Computing
Computing Package Purpose
R-AXIS 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
R-AXIS data collection