X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 292.0
Details 50mM MES pH 6.5, 150mM NaAc and 8% PEG20K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 159.9 α = 90
b = 67.25 β = 111.5
c = 151.64 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2017-11-04
Diffraction Radiation
Monochromator Protocol
Si (111) Silicon crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.9840 ESRF ID23-1

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
2.62 78.78 98.7 0.128 -- -- 3.0 -- 44773 -- -- 48.1
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)
2.62 2.71 98.2 0.859 -- -- 2.8 --

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 2.62 19.977 -- 1.34 -- 44625 2289 98.44 -- 0.226 0.224 0.2651 --
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 2.62 2.6768 -- 159 2593 0.3853 0.4138 0.0 98.0
X Ray Diffraction 2.6768 2.739 -- 140 2560 0.367 0.4042 0.0 97.0
X Ray Diffraction 2.739 2.8073 -- 140 2681 0.3368 0.3689 0.0 99.0
X Ray Diffraction 2.8073 2.883 -- 160 2606 0.3103 0.3426 0.0 99.0
X Ray Diffraction 2.883 2.9675 -- 143 2635 0.2959 0.315 0.0 99.0
X Ray Diffraction 2.9675 3.063 -- 143 2693 0.2838 0.3071 0.0 99.0
X Ray Diffraction 3.063 3.172 -- 123 2592 0.2699 0.3097 0.0 98.0
X Ray Diffraction 3.172 3.2985 -- 140 2636 0.2538 0.2874 0.0 98.0
X Ray Diffraction 3.2985 3.4479 -- 148 2602 0.2457 0.3149 0.0 97.0
X Ray Diffraction 3.4479 3.6287 -- 134 2651 0.2339 0.2958 0.0 99.0
X Ray Diffraction 3.6287 3.8545 -- 140 2663 0.2196 0.2839 0.0 99.0
X Ray Diffraction 3.8545 4.1496 -- 134 2691 0.2038 0.2452 0.0 99.0
X Ray Diffraction 4.1496 4.5627 -- 146 2605 0.1779 0.2076 0.0 97.0
X Ray Diffraction 4.5627 5.2127 -- 146 2697 0.1754 0.2496 0.0 100.0
X Ray Diffraction 5.2127 6.5292 -- 150 2668 0.1945 0.2205 0.0 98.0
X Ray Diffraction 6.5292 19.9778 -- 143 2763 0.1605 0.1817 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.9482
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8625
Nucleic Acid Atoms 529
Heterogen Atoms 33
Solvent Atoms 15

Software

Software
Software Name Purpose
PHENIX refinement
PDB_EXTRACT data extraction version: 3.24
XDS data reduction
XSCALE data scaling
PHASER phasing