X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 20% PEG w/v 1500, 0.1M Tris, 0.1M Ammonium Sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.27 α = 90
b = 72.27 β = 90
c = 140.37 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2011-11-15
Diffraction Radiation
Monochromator Protocol
monochromator (horizontally side diffracting Silicon 111 crystal) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2

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
2.5 37.47 95.3 -- -- -- -- -- 14192 0.0 0.0 --
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)
2.5 2.64 98.5 -- -- -- -- --

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 2.5 37.475 -- 0.0 14351 14192 715 98.89 -- 0.1744 0.1722 0.2198 --
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 2.5 2.6933 -- 147 2670 0.2058 0.2749 -- 98.0
X Ray Diffraction 2.6933 2.9643 -- 154 2652 0.1934 0.2649 -- 99.0
X Ray Diffraction 2.9643 3.393 -- 152 2683 0.1723 0.2427 -- 99.0
X Ray Diffraction 3.393 4.2738 -- 121 2739 0.167 0.1911 -- 99.0
X Ray Diffraction 4.2738 37.4796 -- 141 2733 0.1607 0.1924 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 1.871
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.871
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.742
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.074
f_dihedral_angle_d 13.103
f_angle_d 1.09
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2109
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 84

Software

Computing
Computing Package Purpose
marccd 225 Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
marccd version: 225 data collection