X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 10 mg/mL protein, 0.1 M sodium acetate at pH 6.5, 25% PEG 3350, 0.2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.35 α = 90
b = 118.21 β = 90
c = 63.92 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-04-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-BM-B 1.0 APS 23-BM-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
2.3 20 99.9 -- -- -- -- 37126 37089 3.5 3.5 --
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 -- 99.0 -- 0.496 -- 5.7 --

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 2.3 19.969 -- 1.34 36133 37089 1860 99.96 0.1904 0.1882 0.1882 0.2325 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 2.3001 2.3622 -- 156 2661 0.2119 0.2793 -- 100.0
X Ray Diffraction 2.3622 2.4316 -- 135 2660 0.2082 0.2754 -- 100.0
X Ray Diffraction 2.4316 2.51 -- 150 2647 0.2107 0.3045 -- 100.0
X Ray Diffraction 2.51 2.5995 -- 157 2676 0.2004 0.2549 -- 100.0
X Ray Diffraction 2.5995 2.7033 -- 152 2667 0.1974 0.2508 -- 100.0
X Ray Diffraction 2.7033 2.826 -- 138 2690 0.1925 0.2302 -- 100.0
X Ray Diffraction 2.826 2.9746 -- 128 2716 0.203 0.2739 -- 100.0
X Ray Diffraction 2.9746 3.1603 -- 148 2689 0.2013 0.277 -- 100.0
X Ray Diffraction 3.1603 3.4032 -- 109 2758 0.1922 0.2505 -- 100.0
X Ray Diffraction 3.4032 3.7436 -- 148 2714 0.1765 0.2068 -- 100.0
X Ray Diffraction 3.7436 4.2807 -- 132 2743 0.1684 0.2047 -- 100.0
X Ray Diffraction 4.2807 5.3757 -- 159 2774 0.1647 0.2045 -- 100.0
X Ray Diffraction 5.3757 19.9693 -- 148 2878 0.2034 0.2242 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.5061
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -12.0005
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 14.5066
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.093
f_dihedral_angle_d 16.676
f_angle_d 1.303
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4794
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 243

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
phaser Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
phaser model building
HKL-2000 data collection