X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Lipidic Cubic Phase
pH 7
Temperature 293.0
Details 100 mM HEPES, pH 7.0, 300 mM lithium sulfate, 7.5% DMSO, 30-38% PEG400 in monoolein:cholesterol mixed in a 10:1 ratio, LIPIDIC CUBIC PHASE, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.88 α = 90
b = 174.73 β = 107.84
c = 68.35 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 78
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Mirrors 2011-11-30
Diffraction Radiation
Monochromator Protocol
Double crystal cryo-cooled Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-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
2.8 30.5 99.0 0.144 -- -- 5.8 -- 19145 -- -3.0 --
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 2.9 99.3 0.788 -- 1.8 5.5 1907

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 30.488 -- 1.37 -- 18974 946 97.54 -- 0.2347 0.2326 0.2753 RANDOM
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 2.8 2.9475 -- 122 2355 0.3295 0.3621 -- 89.0
X Ray Diffraction 2.9475 3.132 -- 139 2614 0.2897 0.3318 -- 99.0
X Ray Diffraction 3.132 3.3736 -- 136 2603 0.2689 0.3232 -- 99.0
X Ray Diffraction 3.3736 3.7126 -- 136 2607 0.2328 0.3052 -- 99.0
X Ray Diffraction 3.7126 4.2485 -- 139 2605 0.2089 0.2381 -- 99.0
X Ray Diffraction 4.2485 5.348 -- 136 2608 0.2176 0.2445 -- 99.0
X Ray Diffraction 5.348 30.4897 -- 138 2636 0.2157 0.2695 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 23.1886
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 9.0174
Anisotropic B[2][2] -18.4026
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.786
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.057
f_dihedral_angle_d 12.615
f_angle_d 0.928
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3476
Nucleic Acid Atoms 0
Heterogen Atoms 177
Solvent Atoms 37

Software

Computing
Computing Package Purpose
Blu-Ice Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.2_869) refinement
PHASER model building
Blu-Ice data collection