X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.0
Details 10% glycerol, 15% PEG6000, 0.1M CH3COOK, 6% methylpentanediol, 5 mM beta-mercaptoethanol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 191.51 α = 90
b = 106.43 β = 107.79
c = 250.96 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 80
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2018-06-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 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
4.3 48 94.94 -- -- -- 6.6 -- 31390 -- -- 158.44
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)
4.3 4.5 53.46 -- -- 0.92 -- --

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 4.3 47.79 -- 1.33 -- 31390 1546 95.02 -- 0.2666 0.2627 0.3384 --
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 4.3 4.44 -- 68 1438 0.3389 0.436 -- 50.59
X Ray Diffraction 4.44 4.6 -- 137 2732 0.3278 0.3795 -- 96.6
X Ray Diffraction 4.6 4.78 -- 151 2853 0.3048 0.3715 -- 99.77
X Ray Diffraction 4.78 5.0 -- 119 2849 0.2858 0.326 -- 99.93
X Ray Diffraction 5.0 5.26 -- 151 2809 0.2787 0.3361 -- 99.8
X Ray Diffraction 5.26 5.59 -- 173 2812 0.2798 0.3805 -- 99.63
X Ray Diffraction 5.59 6.02 -- 145 2846 0.2628 0.35 -- 99.83
X Ray Diffraction 6.02 6.63 -- 131 2877 0.2698 0.3401 -- 99.97
X Ray Diffraction 6.63 7.58 -- 150 2838 0.2564 0.3216 -- 99.83
X Ray Diffraction 7.58 9.54 -- 166 2858 0.2413 0.3252 -- 99.93
X Ray Diffraction 9.54 47.79 -- 155 2932 0.2372 0.3227 -- 98.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 244.02
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.9808
f_dihedral_angle_d 22.4439
f_bond_d 0.0042
f_chiral_restr 0.0538
f_plane_restr 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19623
Nucleic Acid Atoms 0
Heterogen Atoms 186
Solvent Atoms 0

Software

Software
Software Name Purpose
PHENIX refinement version: 1.13_2998
XDS data reduction
XDS data scaling
PHASER phasing