X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 298.0
Details 1.06 M sodium malonate, pH 6.0, 0.1 M Tris-HCl, pH 7.5, 0.13 M potassium/sodium phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.43 α = 90
b = 88.43 β = 90
c = 28.94 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-06-21
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA

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
2.33 44.2 99.9 0.052 0.052 -- 9.76 -- 5963 0.0 0.0 --
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)
2.33 2.43 99.4 0.868 0.868 1.2 9.9 --

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 2.33 38.293 -- 1.38 -- 5726 260 99.91 -- 0.1794 0.1769 0.2338 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 2.33 2.9358 -- 117 2702 0.272 0.3757 -- 100.0
X Ray Diffraction 2.9358 38.2986 -- 143 2764 0.162 0.2136 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.062
f_dihedral_angle_d 16.066
f_plane_restr 0.005
f_bond_d 0.007
f_angle_d 1.064
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 585
Nucleic Acid Atoms 94
Heterogen Atoms 0
Solvent Atoms 11

Software

Software
Software Name Purpose
beamline data collection version: software
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.8_1069)
XDS data reduction version: (VERSION March 15
2012) data reduction
SADABS data scaling