X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 298.0
Details 20% MPD, 0.1M Na Cacodylate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 351.39 α = 90
b = 351.39 β = 90
c = 351.39 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2003-02-12
Diffraction Radiation
Monochromator Protocol
Diamond(111) double-bounce monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B 1.107 APS 14-ID-B

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
3.5 20 68.0 0.098 0.098 -- 1.6 123514 123514 0.0 0.0 76.4
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)
3.5 3.62 52.6 0.436 0.436 1.38 1.6 9414

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 + NCS averaging 3.5 20.0 0.0 0.0 123514 104679 1065 62.4 0.313 0.313 0.313 0.316 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 3.5 3.65 9937 109 -- 0.521 0.475 -- 53.0
X Ray Diffraction 3.65 4.08 21064 231 -- 0.458 0.425 -- 56.0
X Ray Diffraction 4.08 4.71 23706 235 -- 0.343 0.324 -- 61.0
X Ray Diffraction 4.71 5.77 22276 237 -- 0.297 0.31 -- 66.0
X Ray Diffraction 5.77 8.16 18558 176 -- 0.207 0.215 -- 71.0
X Ray Diffraction 8.16 20.0 9129 77 -- 0.245 0.284 -- 68.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model individual isotropic
Mean Isotropic B 96.7
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.9
c_bond_d 0.011307
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.8
Luzzati Sigma A (Observed) 1.6
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.7
Luzzati Sigma A (R-Free Set) 1.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4108
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

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