X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details 9% PEG 3350, 0.1M potassium thiocyanate, 0.05M bis-Tris propane

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.22 α = 90
b = 84.04 β = 90
c = 92.97 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2018-01-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU

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
1.8 47.74 99.1 0.05 -- -- 6.8 -- 54004 -- -- 31.26
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)
1.8 1.84 98.3 0.576 -- -- 6.9 --

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 1.8 47.736 -- 1.34 -- 53942 2657 98.88 -- 0.1789 0.1771 0.2145 --
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 1.8 1.8327 -- 128 2631 0.2328 0.2841 0.0 98.0
X Ray Diffraction 1.8327 1.868 -- 134 2675 0.2148 0.2568 0.0 98.0
X Ray Diffraction 1.868 1.9061 -- 154 2618 0.2042 0.2574 0.0 98.0
X Ray Diffraction 1.9061 1.9476 -- 136 2615 0.2003 0.2244 0.0 98.0
X Ray Diffraction 1.9476 1.9929 -- 141 2657 0.189 0.2322 0.0 98.0
X Ray Diffraction 1.9929 2.0427 -- 118 2672 0.1787 0.2178 0.0 99.0
X Ray Diffraction 2.0427 2.0979 -- 142 2646 0.1811 0.234 0.0 99.0
X Ray Diffraction 2.0979 2.1597 -- 140 2699 0.1738 0.1816 0.0 98.0
X Ray Diffraction 2.1597 2.2294 -- 117 2649 0.1747 0.2199 0.0 99.0
X Ray Diffraction 2.2294 2.3091 -- 137 2707 0.1706 0.2106 0.0 99.0
X Ray Diffraction 2.3091 2.4015 -- 136 2692 0.1774 0.2091 0.0 99.0
X Ray Diffraction 2.4015 2.5108 -- 145 2685 0.1718 0.2139 0.0 99.0
X Ray Diffraction 2.5108 2.6432 -- 156 2695 0.1753 0.2035 0.0 99.0
X Ray Diffraction 2.6432 2.8088 -- 142 2700 0.1846 0.2283 0.0 99.0
X Ray Diffraction 2.8088 3.0256 -- 138 2719 0.1849 0.2357 0.0 99.0
X Ray Diffraction 3.0256 3.33 -- 138 2747 0.1815 0.2115 0.0 100.0
X Ray Diffraction 3.33 3.8117 -- 140 2775 0.1731 0.2331 0.0 100.0
X Ray Diffraction 3.8117 4.8016 -- 154 2780 0.1542 0.1931 0.0 100.0
X Ray Diffraction 4.8016 47.7529 -- 161 2923 0.1851 0.2047 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.4453
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3808
Nucleic Acid Atoms 75
Heterogen Atoms 90
Solvent Atoms 313

Software

Software
Software Name Purpose
Aimless data scaling version: 0.7.2
PHENIX refinement version: 1.13_2998
PDB_EXTRACT data extraction version: 3.24
XDS data reduction
MOLREP phasing