X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.75
Temperature 298.0
Details 0.2 M KCl, 0.05 M HEPES/NaOH pH7.75, 33% pentaerythritol propoxylate 426 The affinity tag was cleaved by thrombin. This cleavage was just partial according to a SDS-PAGE analysis.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 117.3 α = 90
b = 117.3 β = 90
c = 137.05 γ = 120
Symmetry
Space Group P 3 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M-F -- 2015-05-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.000000 SLS X06DA

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
3.32 81.61 98.8 0.099 -- -- 10.04 -- 15949 -- -- --
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)
3.32 3.52 92.5 1.071 -- 2.18 9.469 --

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 3.323 81.613 -- 177.68 -- 15948 1120 98.79 -- 0.2491 0.2404 0.2654 --
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 3.3263 3.4777 -- 135 1703 0.3186 0.3131 0.0 85.0
X Ray Diffraction 3.4777 3.661 -- 141 1846 0.3279 0.2994 0.0 93.0
X Ray Diffraction 3.661 3.8903 -- 140 1840 0.2933 0.2854 0.0 93.0
X Ray Diffraction 3.8903 4.1906 -- 145 1870 0.2684 0.2776 0.0 93.0
X Ray Diffraction 4.1906 4.6122 -- 137 1849 0.2723 0.3323 0.0 93.0
X Ray Diffraction 4.6122 5.2791 -- 138 1867 0.2512 0.25 0.0 93.0
X Ray Diffraction 5.2791 6.6495 -- 138 1893 0.2665 0.3028 0.0 93.0
X Ray Diffraction 6.6495 56.8185 -- 144 1944 0.1938 0.243 0.0 93.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 158.041
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 10.222
f_plane_restr 0.004
f_bond_d 0.003
f_chiral_restr 0.043
f_angle_d 0.649
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5298
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 0

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHASER phasing
PHENIX refinement version: 1.13-2998
PDB_EXTRACT data extraction version: 3.24