X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Lipidic Cubic Phase
pH 6.5
Temperature 293.0
Details 38-40% PEG 400, 100 mM Mg (CHO2)2, 50 mM maltose, 100 mM ADA

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.46 α = 90
b = 119.49 β = 103.75
c = 53.91 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2014-12-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU

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
2.4 40 94.6 0.13 -- -- 3.2 -- 22422 -- -- --
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)
2.4 2.49 91.4 0.351 -- 3.6 2.8 --

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 2.4 33.272 -- 1.35 -- 22393 1145 93.78 -- 0.1832 0.181 0.2236 --
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 2.3808 2.4891 -- 120 2424 0.1798 0.2391 -- 86.0
X Ray Diffraction 2.4891 2.6203 -- 139 2683 0.1727 0.2199 -- 95.0
X Ray Diffraction 2.6203 2.7844 -- 162 2693 0.1777 0.2413 -- 96.0
X Ray Diffraction 2.7844 2.9992 -- 137 2743 0.1663 0.2166 -- 96.0
X Ray Diffraction 2.9992 3.3008 -- 147 2693 0.1863 0.2466 -- 96.0
X Ray Diffraction 3.3008 3.7779 -- 152 2703 0.1838 0.208 -- 96.0
X Ray Diffraction 3.7779 4.7575 -- 139 2666 0.1895 0.2177 -- 94.0
X Ray Diffraction 4.7575 33.2752 -- 149 2643 0.1778 0.2232 -- 92.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_chiral_restr 0.039
f_angle_d 1.086
f_dihedral_angle_d 14.024
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3593
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 36

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: 1.9_1692)