X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 289.0
Details 8.5% PEG 6000, 0.1M MES, 1mM DTT, 1mM EDTA, 3% DMSO, 10% Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.43 α = 90
b = 96.74 β = 102.73
c = 67.72 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2009-09-16
Diffraction Radiation
Monochromator Protocol
YALE MIRRORS SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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 27.28 100.0 -- -- -- -- -- 33503 2.0 2.0 30.32
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 2.32 100.0 -- -- -- -- --

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 27.278 -- 1.35 -- 33470 2000 99.96 0.206 0.1916 0.1891 0.2306 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 2.2001 2.2551 -- 142 2236 0.2015 0.2629 -- 100.0
X Ray Diffraction 2.2551 2.316 -- 141 2221 0.1948 0.2588 -- 100.0
X Ray Diffraction 2.316 2.3841 -- 143 2250 0.2023 0.262 -- 100.0
X Ray Diffraction 2.3841 2.461 -- 143 2234 0.194 0.267 -- 100.0
X Ray Diffraction 2.461 2.5489 -- 141 2244 0.1978 0.2571 -- 100.0
X Ray Diffraction 2.5489 2.6509 -- 142 2218 0.1901 0.2421 -- 100.0
X Ray Diffraction 2.6509 2.7714 -- 143 2254 0.1894 0.2491 -- 100.0
X Ray Diffraction 2.7714 2.9174 -- 144 2259 0.1851 0.259 -- 100.0
X Ray Diffraction 2.9174 3.0999 -- 142 2244 0.1825 0.2247 -- 100.0
X Ray Diffraction 3.0999 3.3389 -- 142 2244 0.1726 0.1982 -- 100.0
X Ray Diffraction 3.3389 3.6742 -- 143 2239 0.1674 0.2014 -- 100.0
X Ray Diffraction 3.6742 4.2042 -- 144 2272 0.1726 0.198 -- 100.0
X Ray Diffraction 4.2042 5.2905 -- 143 2259 0.1769 0.2163 -- 100.0
X Ray Diffraction 5.2905 27.2799 -- 147 2296 0.2059 0.2187 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.3825
Anisotropic B[1][1] 1.7066
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.9283
Anisotropic B[2][2] 3.2846
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.9912
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.919
f_bond_d 0.005
f_plane_restr 0.003
f_chiral_restr 0.062
f_dihedral_angle_d 15.812
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4703
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 168

Software

Software
Software Name Purpose
CrystalClear data collection
PHASES phasing
PHENIX refinement version: (phenix.refine)
MOSFLM data reduction
SCALA data scaling