X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details 0.1M MES pH 6.0, 12% PEG3350, 0.1M NH4NO3, EVAPORATION, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.48 α = 90
b = 102.48 β = 90
c = 59.99 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA

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
2.7 20 100.0 0.086 -- -- 7.46 8618 8618 0.0 0.0 --

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 2.7 19.625 -- 1.38 -- 8616 408 99.91 -- 0.2196 0.2162 0.287 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 2.7005 3.09 -- 133 2698 0.336 0.408 -- 100.0
X Ray Diffraction 3.09 3.888 -- 146 2718 0.2186 0.3367 -- 100.0
X Ray Diffraction 3.888 19.6259 -- 129 2792 0.1997 0.2529 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 93.8221
Anisotropic B[1][1] 10.1464
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 10.1464
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -20.2929
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.314
f_plane_restr 0.005
f_chiral_restr 0.061
f_angle_d 0.948
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2062
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DTREK Data Reduction (intensity integration)
DTREK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek data reduction
D*trek version: 9.9.3L data collection