X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 298.0
Details 3.4 M ammonium sulfate, 0.1 M sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 25.02 α = 90
b = 46.34 β = 96.9
c = 28.27 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2011-01-01
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.000 SSRL BL12-2

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
1.23 46.34 97.9 0.058 -- -- 4.2 -- 18288 -- -3.0 11.91
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)
1.23 1.26 94.6 0.609 -- 2.05 3.87 1302

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
SAD 1.23 24.839 -- 1.39 -- 18274 1089 97.89 -- 0.1782 0.1766 0.2039 Random 6%
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 1.2299 1.2859 -- 141 2084 0.3097 0.3587 -- 96.0
X Ray Diffraction 1.2859 1.3537 -- 121 2161 0.2519 0.2723 -- 99.0
X Ray Diffraction 1.3537 1.4385 -- 116 2153 0.1984 0.2431 -- 98.0
X Ray Diffraction 1.4385 1.5496 -- 135 2202 0.1649 0.1914 -- 99.0
X Ray Diffraction 1.5496 1.7055 -- 153 2114 0.148 0.2 -- 98.0
X Ray Diffraction 1.7055 1.9522 -- 154 2140 0.1611 0.1714 -- 98.0
X Ray Diffraction 1.9522 2.4592 -- 134 2155 0.1656 0.2108 -- 98.0
X Ray Diffraction 2.4592 24.8438 -- 135 2176 0.1714 0.187 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Mixed isotropic and anisotropic
Anisotropic B[1][1] -0.4035
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.8457
Anisotropic B[2][2] -1.177
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.5804
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.078
f_dihedral_angle_d 13.637
f_angle_d 1.082
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 655
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 86

Software

Computing
Computing Package Purpose
Blu-Ice Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
SOLVE Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
SOLVE model building
Blu-Ice data collection