X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details 2.4 M SODIUM MALONATE PH 7.0 THE CRYSTALS WERE AIR-DRIED BEFORE FREEZING TO DEHYDRATE.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.94 α = 90
b = 85.94 β = 90
c = 85.29 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 173
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r MIRRORS 2011-12-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 -- Diamond I04

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
2.8 74.4 99.8 0.08 -- -- 5.8 -- 9292 -- 0.0 84.06
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)
2.8 2.95 100.0 0.67 -- 1.3 6.0 --

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
MOLECULAR REPLACEMENT 2.8 28.13 -- 1.35 -- 9292 442 99.83 -- 0.2079 0.2065 0.2357 --
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 2.8002 3.205 -- 148 2893 0.2595 0.3136 -- 100.0
X Ray Diffraction 3.205 4.036 -- 144 2929 0.2162 0.2347 -- 100.0
X Ray Diffraction 4.036 28.1318 -- 150 3028 0.1928 0.2209 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 68.75
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.068
f_bond_d 0.007
f_angle_d 1.073
f_dihedral_angle_d 16.638
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1294
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 16

Software

Software
Software Name Purpose
PHENIX refinement version: (PHENIX.REFINE)
XDS data reduction
SCALA data scaling
PHASER phasing