X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details 20% PEG 3350, 0.2M Ammonium Sulfate, 0.1M Bis-Tris pH 6.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.2 α = 90
b = 99.2 β = 90
c = 80.07 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2018-07-08
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.9793 Diamond I03

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
1.93 85.91 100.0 0.186 -- -- 19.2 -- 665286 -- -- 29.38
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)
1.93 1.96 100.0 2.342 -- 1.4 19.4 --

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 1.93 85.91 -- 1.34 -- 34552 1655 99.92 -- 0.2004 0.1986 0.2352 --
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 1.93 1.99 -- 155 2674 0.2677 0.3053 -- 99.65
X Ray Diffraction 1.99 2.05 -- 128 2729 0.258 0.313 -- 100.0
X Ray Diffraction 2.05 2.12 -- 132 2705 0.2403 0.277 -- 99.79
X Ray Diffraction 2.12 2.21 -- 144 2694 0.2359 0.3057 -- 100.0
X Ray Diffraction 2.21 2.31 -- 125 2738 0.232 0.2793 -- 99.97
X Ray Diffraction 2.31 2.43 -- 117 2735 0.2257 0.2806 -- 99.93
X Ray Diffraction 2.43 2.58 -- 123 2732 0.2268 0.2868 -- 99.86
X Ray Diffraction 2.58 2.78 -- 153 2718 0.2174 0.2576 -- 100.0
X Ray Diffraction 2.78 3.06 -- 171 2712 0.2059 0.2652 -- 99.97
X Ray Diffraction 3.06 3.51 -- 142 2767 0.1835 0.219 -- 100.0
X Ray Diffraction 3.51 4.42 -- 139 2780 0.1599 0.1778 -- 100.0
X Ray Diffraction 4.42 85.99 -- 126 2913 0.1809 0.198 -- 99.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.38
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.7497
f_dihedral_angle_d 15.3523
f_bond_d 0.0057
f_plane_restr 0.0053
f_chiral_restr 0.0499
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3197
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 365

Software

Software
Software Name Purpose
xia2 data reduction version: 1.10.2-g9c23cb36c-release
xia2 data scaling version: 1.10.2-g9c23cb36c-release
Aimless data scaling version: 0.7.1
PHASER phasing version: 2.8.1
PHENIX refinement version: 1.13-2998