X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 3.9
Temperature 277.0
Details 10-12% PEG 4000, 225 mM ammonium sulfate, 50 mM sodium acetate buffer (pH 3.9 - 4.1), VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 182.03 α = 90
b = 133.62 β = 102.57
c = 161.43 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD DECTRIS PILATUS 6M K-B focusing mirrors 2011-03-25
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 0.9795 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
3.19 30 97.5 0.068 -- -- -- 63002 61417 -- -3.0 88.969
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)
3.19 3.38 92.9 0.707 -- 1.83 -- --

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 3.19 29.857 -- 1.99 -- 61291 999 97.54 -- 0.2045 0.2039 0.243 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 3.1904 3.3584 -- 133 8122 0.3038 0.3157 -- 93.0
X Ray Diffraction 3.3584 3.5685 -- 142 8533 0.2393 0.2566 -- 97.0
X Ray Diffraction 3.5685 3.8435 -- 145 8759 0.1866 0.2378 -- 99.0
X Ray Diffraction 3.8435 4.2293 -- 145 8714 0.1606 0.2188 -- 99.0
X Ray Diffraction 4.2293 4.8391 -- 143 8625 0.1412 0.1953 -- 98.0
X Ray Diffraction 4.8391 6.0882 -- 145 8768 0.2015 0.1987 -- 99.0
X Ray Diffraction 6.0882 29.858 -- 146 8771 0.2403 0.299 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 88.5796
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.494
f_plane_restr 0.008
f_chiral_restr 0.08
f_angle_d 1.3
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12661
Nucleic Acid Atoms 0
Heterogen Atoms 698
Solvent Atoms 56

Software

Computing
Computing Package Purpose
BlueIce Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction