X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 6.7
Temperature 293.0
Details 2.3 M Na/K phosphate, pH 6.7, SMALL TUBES, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.6 α = 90
b = 53.6 β = 90
c = 191.2 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2008-03-30
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
1.8 99 98.1 -- 0.05 -- 4.1 27031 26524 0.0 -3.0 --
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)
1.8 1.86 96.9 -- 0.164 12.5 4.0 --

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
FOURIER SYNTHESIS 1.8 37.178 -- 0.0 26922 26279 1988 97.61 0.1729 0.1729 0.1703 0.2048 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 1.7998 1.8448 -- 137 1655 0.2374 0.2837 -- 95.0
X Ray Diffraction 1.8448 1.8947 -- 137 1648 0.1994 0.2452 -- 95.0
X Ray Diffraction 1.8947 1.9505 -- 134 1649 0.1611 0.2162 -- 96.0
X Ray Diffraction 1.9505 2.0134 -- 138 1677 0.1603 0.2141 -- 96.0
X Ray Diffraction 2.0134 2.0854 -- 138 1672 0.1614 0.2089 -- 96.0
X Ray Diffraction 2.0854 2.1688 -- 137 1709 0.1602 0.2149 -- 97.0
X Ray Diffraction 2.1688 2.2675 -- 140 1701 0.1683 0.2002 -- 98.0
X Ray Diffraction 2.2675 2.3871 -- 141 1729 0.1625 0.2162 -- 98.0
X Ray Diffraction 2.3871 2.5366 -- 143 1750 0.172 0.1872 -- 99.0
X Ray Diffraction 2.5366 2.7324 -- 144 1763 0.1681 0.2186 -- 99.0
X Ray Diffraction 2.7324 3.0073 -- 146 1785 0.171 0.2279 -- 100.0
X Ray Diffraction 3.0073 3.4421 -- 145 1794 0.1653 0.1963 -- 100.0
X Ray Diffraction 3.4421 4.3357 -- 150 1829 0.1456 0.1832 -- 99.0
X Ray Diffraction 4.3357 37.1855 -- 158 1930 0.197 0.1915 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Anisotropic B[1][1] -0.5249
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.5249
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.0497
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.989
f_plane_restr 0.005
f_bond_d 0.027
f_chiral_restr 0.067
f_dihedral_angle_d 12.774
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2190
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 327

Software

Software
Software Name Purpose
CrystalClear data collection
PHENIX model building
PHENIX refinement version: (phenix.refine: 1.6.4_486)
DENZO data reduction
SCALEPACK data scaling
PHENIX phasing