X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details 2 M sodium malonate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.58 α = 90
b = 107.58 β = 90
c = 72.71 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2011-08-15
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.9793, 0.9300 NSLS X25

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
2.1 46.58 100.0 0.083 -- -- 9.8 -- 28120 -- -- --
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)
2.1 2.14 100.0 0.558 -- 3.0 10.0 --

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
SAD 2.099 46.584 -- 1.38 -- 28096 1414 99.95 -- 0.1674 0.1652 0.2086 --
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 2.099 2.1741 -- 127 2659 0.1738 0.2201 -- 100.0
X Ray Diffraction 2.1741 2.2611 -- 150 2630 0.1719 0.214 -- 100.0
X Ray Diffraction 2.2611 2.364 -- 122 2678 0.1708 0.2662 -- 100.0
X Ray Diffraction 2.364 2.4886 -- 153 2644 0.1739 0.2172 -- 100.0
X Ray Diffraction 2.4886 2.6446 -- 142 2663 0.1807 0.2471 -- 100.0
X Ray Diffraction 2.6446 2.8487 -- 142 2655 0.1875 0.2278 -- 100.0
X Ray Diffraction 2.8487 3.1353 -- 137 2667 0.1837 0.2583 -- 100.0
X Ray Diffraction 3.1353 3.5889 -- 146 2687 0.172 0.2118 -- 100.0
X Ray Diffraction 3.5889 4.521 -- 166 2655 0.1384 0.1733 -- 100.0
X Ray Diffraction 4.521 46.5954 -- 129 2744 0.1596 0.189 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.003
f_bond_d 0.008
f_chiral_restr 0.046
f_dihedral_angle_d 13.524
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3230
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 160

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: 1.8.4_1496)
DENZO data reduction
SCALEPACK data scaling