X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Lipidic Cubic Phase
pH 6.5
Temperature 293.0
Details 350-450 mM potassium nitrate, 100 mM MES, 1 mM TCEP, 10 mM phosphonoformate, 0.01 mM BI167107, 18-22% PEG400. Crystals were grown in a 10:1 (w:w) MAG 7.7:cholesterol lipid mix. , pH 6.5, Lipidic cubic phase, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.34 α = 90
b = 64.56 β = 91.67
c = 131.24 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 78
2 78
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD Mirrors 2011-04-24
CCD MARMOSAIC 300 mm CCD Mirrors 2011-04-15
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal SINGLE WAVELENGTH
Si(111) double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B

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
3.2 50 91.2 0.156 -- -- 6.5 -- 31685 -- -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)
3.2 3.26 53.9 0.553 -- 1.81 5.0 943

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 3.2 40.675 -- 1.35 -- 31073 1557 92.82 -- 0.2282 0.2255 0.2772 --
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 3.2 3.3033 -- 100 1768 0.3098 0.3642 -- 62.0
X Ray Diffraction 3.3033 3.4213 -- 116 2263 0.3156 0.407 -- 79.0
X Ray Diffraction 3.4213 3.5582 -- 122 2565 0.3027 0.3454 -- 89.0
X Ray Diffraction 3.5582 3.72 -- 130 2727 0.2844 0.3503 -- 95.0
X Ray Diffraction 3.72 3.916 -- 137 2829 0.223 0.2666 -- 98.0
X Ray Diffraction 3.916 4.1611 -- 153 2855 0.19 0.2457 -- 99.0
X Ray Diffraction 4.1611 4.482 -- 170 2846 0.1618 0.2004 -- 100.0
X Ray Diffraction 4.482 4.9324 -- 177 2867 0.1663 0.2265 -- 100.0
X Ray Diffraction 4.9324 5.6445 -- 128 2933 0.2076 0.2562 -- 100.0
X Ray Diffraction 5.6445 7.1053 -- 144 2916 0.2525 0.3149 -- 99.0
X Ray Diffraction 7.1053 40.6785 -- 180 2947 0.2297 0.2856 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -7.0864
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.9451
Anisotropic B[2][2] 2.9389
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.7946
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.051
f_dihedral_angle_d 12.385
f_angle_d 0.709
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10247
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 0

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_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
Phaser model building
Blu-Ice data collection