X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 0.8 M Li2SO4 100 mM TRIS 5mM CaCl2 10 mM NiCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.38 α = 90
b = 114.38 β = 90
c = 122.32 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2009-06-17
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-1

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
2.5 37.7 99.1 -- 0.048 -- 3.5 16748 16748 0.0 0.0 64.5
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)
2.5 2.55 99.8 -- -- -- -- --

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 2.5 37.704 -- 0.0 16748 16748 839 99.18 0.2374 0.2374 0.2354 0.2742 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 2.5001 2.6567 -- 138 2594 0.3257 0.358 -- 100.0
X Ray Diffraction 2.6567 2.8617 -- 137 2607 0.3067 0.3778 -- 100.0
X Ray Diffraction 2.8617 3.1496 -- 138 2618 0.2851 0.3117 -- 99.0
X Ray Diffraction 3.1496 3.605 -- 139 2651 0.2609 0.3117 -- 100.0
X Ray Diffraction 3.605 4.5407 -- 141 2668 0.204 0.2517 -- 99.0
X Ray Diffraction 4.5407 37.7084 -- 146 2771 0.21 0.2336 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 3.2306
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.2306
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.4613
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.077
f_plane_restr 0.004
f_bond_d 0.008
f_dihedral_angle_d 15.7
f_angle_d 1.135
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1621
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 14

Software

Software
Software Name Purpose
MxDC data collection
PHASER phasing
PHENIX refinement version: (phenix.refine: 1.6.3_473)
XDS data reduction
XSCALE data scaling