X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 292.0
Details 2-2.2 M ammonium sulfate with the pH ranging from 6 to 9 , VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.88 α = 90
b = 63.88 β = 90
c = 105.11 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON MAX II BEAMLINE I911-3 1.0 MAX II I911-3

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
2.25 19.7 99.8 -- 0.066 -- 7.6 -- n/a 2.0 2.0 51.3

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 2.25 19.651 -- 2.0 10824 11568 554 99.98 -- -- 0.2438 0.2427 --
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 2.25 2.4761 -- 125 2751 0.3037 0.2934 -- 100.0
X Ray Diffraction 2.4761 2.8335 -- 153 2727 0.2654 0.2611 -- 100.0
X Ray Diffraction 2.8335 3.5664 -- 142 2756 0.2328 0.2549 -- 100.0
X Ray Diffraction 3.5664 19.6518 -- 134 2780 0.233 0.2212 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 66.0916
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.067
f_dihedral_angle_d 13.402
f_angle_d 1.034
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1262
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 34

Software

Computing
Computing Package Purpose
MXcube Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
Xscale data reduction