X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop Vapor Diffusion
pH 6.5
Temperature 293.0
Details 0.1 M MES, 0.8 M sodium acetate, 0.1 M NaCl, 20% (w/v) ethylene glycol;, pH 6.5, hanging-drop vapor diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.83 α = 90
b = 47.25 β = 102.03
c = 57.64 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r monochromator 2011-11-18
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
synchrotron APS BEAMLINE 19-ID 0.97918 APS 19-ID

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
2.3 50 99.0 0.134 -- -- 3.9 13766 13766 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)
2.3 2.34 94.9 0.388 -- -- 3.4 --

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
FOURIER SYNTHESIS 2.3001 29.654 -- 1.36 13718 13721 673 98.75 -- 0.1798 0.1768 0.238 --
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 2.3001 2.4776 -- 135 2518 0.2129 0.2886 -- 96.0
X Ray Diffraction 2.4776 2.7268 -- 142 2566 0.1967 0.2529 -- 99.0
X Ray Diffraction 2.7268 3.121 -- 127 2621 0.179 0.2552 -- 100.0
X Ray Diffraction 3.121 3.9307 -- 131 2653 0.1639 0.2156 -- 100.0
X Ray Diffraction 3.9307 29.6565 -- 138 2690 0.167 0.2219 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.1165
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.043
f_dihedral_angle_d 14.794
f_angle_d 0.795
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2500
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 158

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction