X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details Bis-Tris propan, CaCl2, PEG 3350, pH 6.0, vapor diffusion, sitting drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.74 α = 90
b = 96.74 β = 90
c = 299.36 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD DECTRIS PILATUS 2M-F -- 2012-06-15
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1000 PHOTON FACTORY BL-1A

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
3.64 48.71 99.6 0.107 -- -- -- -- 18933 -- -3.0 125.88
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)
3.64 3.86 98.1 0.012 -- 2.05 -- --

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 3.641 38.09 -- -- -- 18926 1333 99.67 -- 0.2552 0.2529 0.2875 --
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 3.641 3.7714 -- 117 1670 0.3322 0.3422 -- 97.0
X Ray Diffraction 3.7714 3.9223 -- 150 1712 0.3219 0.3443 -- 100.0
X Ray Diffraction 3.9223 4.1006 -- 135 1732 0.3091 0.3292 -- 100.0
X Ray Diffraction 4.1006 4.3165 -- 123 1736 0.2942 0.364 -- 100.0
X Ray Diffraction 4.3165 4.5865 -- 126 1766 0.2614 0.2823 -- 100.0
X Ray Diffraction 4.5865 4.94 -- 142 1736 0.2457 0.3039 -- 100.0
X Ray Diffraction 4.94 5.4358 -- 117 1762 0.2548 0.2707 -- 100.0
X Ray Diffraction 5.4358 6.2195 -- 130 1790 0.2659 0.334 -- 100.0
X Ray Diffraction 6.2195 7.8247 -- 158 1768 0.2658 0.2552 -- 100.0
X Ray Diffraction 7.8247 38.0922 -- 135 1921 0.2074 0.2499 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 104.901
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.093
f_plane_restr 0.003
f_chiral_restr 0.035
f_angle_d 0.761
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8128
Nucleic Acid Atoms 3146
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
UGUI Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction