X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Temperature 293.0
Details 0.1-0.2M sodium chloride, 100mM sodium phosphate pH 6.0-6.5, 25%-35% PEG 300, Lipidic cubic phase (in meso phase), temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.04 α = 90
b = 71.46 β = 90
c = 172.19 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2012-02-18
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-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
2.2 30 95.6 0.135 -- -- 4.8 28455 27181 1.0 1.0 --
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)
2.2 2.25 85.7 0.575 -- -- 3.3 1585

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 2.2 28.273 -- 0.0 28455 25921 1306 91.01 0.2188 0.2188 0.218 0.235 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 2.1994 2.2874 -- 110 2190 0.3184 0.3808 -- 75.0
X Ray Diffraction 2.2874 2.3915 -- 136 2533 0.2846 0.3101 -- 85.0
X Ray Diffraction 2.3915 2.5175 -- 141 2627 0.2508 0.2611 -- 89.0
X Ray Diffraction 2.5175 2.6751 -- 133 2721 0.2307 0.2337 -- 92.0
X Ray Diffraction 2.6751 2.8814 -- 165 2761 0.2186 0.2455 -- 93.0
X Ray Diffraction 2.8814 3.1711 -- 159 2850 0.2233 0.2713 -- 95.0
X Ray Diffraction 3.1711 3.6291 -- 143 2922 0.2116 0.2553 -- 97.0
X Ray Diffraction 3.6291 4.5692 -- 161 2894 0.184 0.2074 -- 96.0
X Ray Diffraction 4.5692 28.2755 -- 158 3117 0.2078 0.1828 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.5549
Anisotropic B[1][1] 25.201
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.8018
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -16.3993
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.965
f_plane_restr 0.006
f_chiral_restr 0.06
f_angle_d 0.948
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3470
Nucleic Acid Atoms 0
Heterogen Atoms 263
Solvent Atoms 91

Software

Computing
Computing Package Purpose
Locally modified Blu-Ice GUI interface to EPICS control Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
Phenix (phaser) Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction