X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.8
Temperature 277.0
Details 0.1 M HEPES, pH 7.8, 0.2 M MgCl2, 12% PEG8000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.36 α = 90
b = 88.36 β = 90
c = 72.51 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2014-03-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54 -- --

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
1.99 50 99.8 0.059 -- 63.373 20.5 -- 22728 -- -- 23.04
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)
1.99 2.02 97.5 0.219 -- -- 11.6 1072

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 1.991 28.923 -- 1.34 -- 22687 1117 99.71 -- 0.167 0.1646 0.211 --
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 1.9913 2.0819 -- 108 2634 0.1704 0.2727 -- 98.0
X Ray Diffraction 2.0819 2.1916 -- 125 2679 0.1694 0.2225 -- 100.0
X Ray Diffraction 2.1916 2.3289 -- 175 2659 0.1723 0.2342 -- 100.0
X Ray Diffraction 2.3289 2.5086 -- 128 2672 0.1796 0.2239 -- 100.0
X Ray Diffraction 2.5086 2.7608 -- 143 2678 0.186 0.286 -- 100.0
X Ray Diffraction 2.7608 3.1599 -- 146 2706 0.1827 0.2202 -- 100.0
X Ray Diffraction 3.1599 3.9795 -- 131 2726 0.1493 0.1931 -- 100.0
X Ray Diffraction 3.9795 28.9263 -- 161 2816 0.1503 0.1751 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.9813
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.7
f_chiral_restr 0.066
f_plane_restr 0.006
f_angle_d 1.047
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2267
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 213

Software

Software
Software Name Purpose
PHENIX refinement
HKL-2000 data scaling
PHASER phasing version: 2.5.6
PDB_EXTRACT data extraction version: 3.15