X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.25
Temperature 293.0
Details 5% PEG 3000, 0.2 M Zn acetate and 0.1 M sodium acetate pH 5.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.09 α = 90
b = 109.09 β = 90
c = 109.09 γ = 90
Symmetry
Space Group I 2 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2012-06-12
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 1 SSRL BL9-2

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
1.49 38.57 100.0 0.073 -- -- 44.5 -- 35031 -- -- --

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 1.7 38.569 -- 1.36 -- 23875 1362 99.97 -- 0.1909 0.1898 0.2083 --
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 1.7004 1.7612 -- 134 2234 0.2024 0.2156 -- 100.0
X Ray Diffraction 1.7612 1.8317 -- 133 2218 0.2038 0.2722 -- 100.0
X Ray Diffraction 1.8317 1.915 -- 135 2242 0.1931 0.1997 -- 100.0
X Ray Diffraction 1.915 2.016 -- 137 2236 0.1907 0.1885 -- 100.0
X Ray Diffraction 2.016 2.1423 -- 138 2246 0.1865 0.2374 -- 1.01
X Ray Diffraction 2.1423 2.3077 -- 134 2217 0.2009 0.2315 -- 100.0
X Ray Diffraction 2.3077 2.5399 -- 131 2264 0.2115 0.2059 -- 100.0
X Ray Diffraction 2.5399 2.9073 -- 140 2247 0.2016 0.2188 -- 100.0
X Ray Diffraction 2.9073 3.6624 -- 137 2272 0.1892 0.2308 -- 100.0
X Ray Diffraction 3.6624 38.579 -- 143 2337 0.1733 0.1731 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.069
f_dihedral_angle_d 15.706
f_angle_d 1.056
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 957
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 130

Software

Computing
Computing Package Purpose
Web-ice Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
Web-ice data collection