X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 100 mM HEPES pH 7.5, 0.5 M Sodium acetate, 31% PEG 3350, and 1 mM ATP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.89 α = 90
b = 124.54 β = 90
c = 109.14 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2019-04-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2

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
2 39.2 96.0 0.219 -- -- 9.6 -- 44741 -- -- --
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)
2.0 2.05 73.7 1.878 -- 1.0 6.5 --

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 2.0 39.197 -- 1.35 -- 44644 2292 95.63 -- 0.1931 0.1912 0.2272 --
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 2.0001 2.0436 -- 99 1951 0.3372 0.3958 -- 71.0
X Ray Diffraction 2.0436 2.0911 -- 121 2166 0.3071 0.2956 -- 79.0
X Ray Diffraction 2.0911 2.1434 -- 118 2411 0.271 0.3184 -- 88.0
X Ray Diffraction 2.1434 2.2013 -- 147 2611 0.2545 0.2888 -- 96.0
X Ray Diffraction 2.2013 2.2661 -- 125 2752 0.2308 0.2928 -- 100.0
X Ray Diffraction 2.2661 2.3392 -- 162 2745 0.2156 0.2494 -- 100.0
X Ray Diffraction 2.3392 2.4228 -- 149 2753 0.2106 0.2883 -- 100.0
X Ray Diffraction 2.4228 2.5198 -- 157 2720 0.2148 0.2448 -- 100.0
X Ray Diffraction 2.5198 2.6345 -- 140 2716 0.2035 0.2841 -- 99.0
X Ray Diffraction 2.6345 2.7733 -- 149 2779 0.2065 0.2427 -- 100.0
X Ray Diffraction 2.7733 2.947 -- 150 2746 0.1956 0.2086 -- 100.0
X Ray Diffraction 2.947 3.1745 -- 154 2738 0.1909 0.2188 -- 99.0
X Ray Diffraction 3.1745 3.4938 -- 148 2777 0.1689 0.2109 -- 100.0
X Ray Diffraction 3.4938 3.9989 -- 141 2789 0.1537 0.1897 -- 99.0
X Ray Diffraction 3.9989 5.0365 -- 163 2805 0.135 0.1829 -- 100.0
X Ray Diffraction 5.0365 39.2049 -- 169 2893 0.1848 0.1984 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.939
f_bond_d 0.006
f_chiral_restr 0.045
f_angle_d 0.746
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4703
Nucleic Acid Atoms 0
Heterogen Atoms 27
Solvent Atoms 508

Software

Software
Software Name Purpose
PHENIX refinement version: (1.14_3260: ???)
XDS data reduction
Aimless data scaling
PHASER phasing