X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 277.0
Details 20% (w/v) PEGF-4000, 10% 2-propanol, 0.1 M HEPES, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.3 α = 90
b = 60.3 β = 90
c = 96.91 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-11-21
Diffraction Radiation
Monochromator Protocol
two flat Si(111) crystals, mounted in a model DCM from Khozu SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1

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
1.65 50 99.9 0.081 -- -- 8.7 -- 25135 -- -3.0 16.8
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)
1.79 1.89 100.0 0.465 -- 5.43 -- --

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 1.7901 45.972 -- 2.0 -- 19790 1187 99.94 -- 0.1673 0.1653 0.1979 Random selection
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 1.7901 1.8715 -- 146 2280 0.1759 0.2059 -- 100.0
X Ray Diffraction 1.8715 1.9702 -- 145 2285 0.1625 0.2189 -- 100.0
X Ray Diffraction 1.9702 2.0936 -- 148 2308 0.1535 0.1508 -- 100.0
X Ray Diffraction 2.0936 2.2553 -- 146 2288 0.1441 0.1857 -- 100.0
X Ray Diffraction 2.2553 2.4822 -- 147 2310 0.1648 0.2088 -- 100.0
X Ray Diffraction 2.4822 2.8414 -- 148 2319 0.1831 0.2274 -- 100.0
X Ray Diffraction 2.8414 3.5796 -- 150 2353 0.1707 0.1968 -- 100.0
X Ray Diffraction 3.5796 45.9868 -- 157 2460 0.1628 0.194 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.3427
Anisotropic B[1][1] 0.7237
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.7237
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.4473
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.056
f_bond_d 0.006
f_dihedral_angle_d 11.061
f_angle_d 0.889
f_plane_restr 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 31
Solvent Atoms 133

Software

Software
Software Name Purpose
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.15
PHENIX refinement version: (phenix.refine: 1.7.1_743)
Coot model building