X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 283.0
Details Compound soaked into crystal grown in equal volume of 500mM MES buffer (pH 6.0) and 25% MPD

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.89 α = 90
b = 73.37 β = 90
c = 105.12 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 -- 2016-08-13
Diffraction Radiation
Monochromator Protocol
KOHZU DUAL DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1

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
1.5 105.12 99.8 0.066 -- -- 11.7 -- 63695 -- -- 20.9
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)
1.5 1.54 97.4 1.317 -- -- 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 1.5 45.808 -- 1.33 -- 63215 3102 99.14 -- 0.1554 0.1537 0.1904 --
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 1.5 1.5235 -- 137 2306 0.4178 0.4883 0.0 86.0
X Ray Diffraction 1.5235 1.5484 -- 116 2648 0.3287 0.3983 0.0 97.0
X Ray Diffraction 1.5484 1.5751 -- 141 2678 0.2845 0.2718 0.0 99.0
X Ray Diffraction 1.5751 1.6038 -- 171 2700 0.253 0.305 0.0 100.0
X Ray Diffraction 1.6038 1.6346 -- 154 2691 0.2152 0.2394 0.0 100.0
X Ray Diffraction 1.6346 1.668 -- 149 2716 0.2151 0.2636 0.0 100.0
X Ray Diffraction 1.668 1.7043 -- 136 2741 0.1912 0.2603 0.0 100.0
X Ray Diffraction 1.7043 1.7439 -- 136 2759 0.1757 0.2283 0.0 100.0
X Ray Diffraction 1.7439 1.7875 -- 131 2703 0.1658 0.2134 0.0 100.0
X Ray Diffraction 1.7875 1.8359 -- 144 2723 0.1526 0.2056 0.0 100.0
X Ray Diffraction 1.8359 1.8899 -- 130 2756 0.1466 0.1864 0.0 100.0
X Ray Diffraction 1.8899 1.9509 -- 146 2741 0.1459 0.2082 0.0 100.0
X Ray Diffraction 1.9509 2.0206 -- 122 2748 0.1437 0.2038 0.0 100.0
X Ray Diffraction 2.0206 2.1015 -- 136 2754 0.1396 0.1698 0.0 100.0
X Ray Diffraction 2.1015 2.1971 -- 143 2745 0.1346 0.2081 0.0 100.0
X Ray Diffraction 2.1971 2.313 -- 133 2774 0.1341 0.1805 0.0 100.0
X Ray Diffraction 2.313 2.4579 -- 142 2762 0.14 0.1736 0.0 100.0
X Ray Diffraction 2.4579 2.6476 -- 140 2780 0.143 0.1839 0.0 100.0
X Ray Diffraction 2.6476 2.914 -- 152 2770 0.1497 0.1665 0.0 100.0
X Ray Diffraction 2.914 3.3356 -- 152 2797 0.1546 0.1974 0.0 100.0
X Ray Diffraction 3.3356 4.2021 -- 153 2837 0.1404 0.1543 0.0 100.0
X Ray Diffraction 4.2021 45.8293 -- 138 2984 0.1398 0.1703 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.2874
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.419
f_bond_d 0.016
f_chiral_restr 0.075
f_plane_restr 0.008
f_dihedral_angle_d 14.243
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2371
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 226

Software

Software
Software Name Purpose
Aimless data scaling version: 0.5.21
PHASER phasing version: 2.6.1
PHENIX refinement
PDB_EXTRACT data extraction version: 3.22
XDS data reduction