X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.2
Temperature 293.0
Details 0.1M citrate pH4.2, 0.2M sodium chloride, 18% (W/V) PEG 8000

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.26 α = 90
b = 63.26 β = 90
c = 346.7 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M -- 2017-04-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1

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
1.64 57.78 100.0 0.0971 -- -- 18.8 -- 52137 -- -- --
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)
-- -- -- -- -- -- -- --

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 1.64 54.78 -- 1.33 -- 49371 2442 94.99 -- 0.2084 0.2067 0.2398 --
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 1.6402 1.6737 -- 141 2493 0.4308 0.4863 -- 88.0
X Ray Diffraction 1.6737 1.7101 -- 118 2621 0.413 0.4064 -- 92.0
X Ray Diffraction 1.7101 1.7499 -- 135 2561 0.3939 0.4744 -- 91.0
X Ray Diffraction 1.7499 1.7936 -- 118 2637 0.3612 0.3981 -- 93.0
X Ray Diffraction 1.7936 1.8421 -- 145 2623 0.3296 0.345 -- 93.0
X Ray Diffraction 1.8421 1.8963 -- 139 2692 0.3079 0.3537 -- 94.0
X Ray Diffraction 1.8963 1.9575 -- 147 2698 0.2911 0.3252 -- 95.0
X Ray Diffraction 1.9575 2.0275 -- 150 2713 0.2716 0.3613 -- 95.0
X Ray Diffraction 2.0275 2.1087 -- 137 2786 0.2594 0.3283 -- 96.0
X Ray Diffraction 2.1087 2.2047 -- 155 2696 0.2343 0.3131 -- 95.0
X Ray Diffraction 2.2047 2.3209 -- 143 2800 0.2155 0.2378 -- 97.0
X Ray Diffraction 2.3209 2.4663 -- 117 2814 0.2017 0.2577 -- 96.0
X Ray Diffraction 2.4663 2.6567 -- 147 2835 0.2076 0.2375 -- 97.0
X Ray Diffraction 2.6567 2.9241 -- 151 2847 0.2035 0.2562 -- 97.0
X Ray Diffraction 2.9241 3.3471 -- 140 2921 0.2015 0.2212 -- 98.0
X Ray Diffraction 3.3471 4.2168 -- 162 3001 0.1644 0.1973 -- 99.0
X Ray Diffraction 4.2168 54.8106 -- 197 3191 0.1671 0.187 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.072
f_bond_d 0.009
f_dihedral_angle_d 14.308
f_plane_restr 0.005
f_chiral_restr 0.043
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2787
Nucleic Acid Atoms 28
Heterogen Atoms 24
Solvent Atoms 282

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
xia2 data reduction
xia2 data scaling
PHENIX phasing