X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 38% PEG 8000, 100 mM imidazole, 250 mM NaCl. Crystals soaked 30 min in 20 mM 2-oxoglutarate solution

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.52 α = 90
b = 65.37 β = 90
c = 84.57 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-11-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.127 APS 21-ID-D

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
1.87 50 97.2 0.074 -- -- 5.7 -- 19714 -- -- 25.9
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)
1.87 1.94 98.7 0.324 -- -- 5.7 --

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 1.87 37.99 -- 1.37 -- 19681 1440 96.7 -- 0.171 0.168 0.209 --
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 1.863 1.9295 -- 135 1726 0.189 0.2278 -- 93.0
X Ray Diffraction 1.9295 2.0068 -- 145 1823 0.174 0.2152 -- 99.0
X Ray Diffraction 2.0068 2.0981 -- 144 1842 0.1728 0.2231 -- 99.0
X Ray Diffraction 2.0981 2.2087 -- 141 1824 0.1697 0.2155 -- 99.0
X Ray Diffraction 2.2087 2.3471 -- 149 1845 0.1679 0.2252 -- 98.0
X Ray Diffraction 2.3471 2.5283 -- 142 1830 0.1746 0.229 -- 98.0
X Ray Diffraction 2.5283 2.7826 -- 143 1839 0.1836 0.2351 -- 98.0
X Ray Diffraction 2.7826 3.1851 -- 147 1827 0.1793 0.225 -- 97.0
X Ray Diffraction 3.1851 4.0122 -- 143 1838 0.1561 0.2124 -- 95.0
X Ray Diffraction 4.0122 37.9992 -- 151 1847 0.1609 0.1747 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.18
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.045
f_plane_restr 0.006
f_bond_d 0.009
f_dihedral_angle_d 15.172
f_angle_d 1.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1933
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 128

Software

Software
Software Name Purpose
PHENIX refinement version: dev_1839
HKL-2000 data reduction
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data scaling
PHASER phasing