X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 0.24 M sodium malonate pH 7.0, 20 % PEG 3,350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 149.96 α = 90
b = 149.96 β = 90
c = 77.52 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M -- 2018-11-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.873130 ESRF ID23-2

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
2.4 53.89 99.7 0.202 -- -- 10.159 -- 38887 -- -- 48.198
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)
2.4 2.5 99.5 1.618 -- 1.57 10.418 --

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 2.4 53.894 -- 1.34 -- 38885 1945 99.67 -- 0.1995 0.1976 0.2359 --
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 2.4001 2.4601 -- 138 2626 0.2953 0.3312 0.0 100.0
X Ray Diffraction 2.4601 2.5266 -- 137 2609 0.2832 0.3403 0.0 100.0
X Ray Diffraction 2.5266 2.6009 -- 139 2636 0.2823 0.331 0.0 100.0
X Ray Diffraction 2.6009 2.6849 -- 138 2608 0.2599 0.2856 0.0 100.0
X Ray Diffraction 2.6849 2.7808 -- 137 2611 0.2411 0.2777 0.0 100.0
X Ray Diffraction 2.7808 2.8922 -- 139 2636 0.235 0.2777 0.0 100.0
X Ray Diffraction 2.8922 3.0238 -- 138 2634 0.2359 0.2555 0.0 100.0
X Ray Diffraction 3.0238 3.1832 -- 139 2637 0.2393 0.2903 0.0 99.0
X Ray Diffraction 3.1832 3.3826 -- 138 2625 0.2093 0.3133 0.0 100.0
X Ray Diffraction 3.3826 3.6437 -- 139 2642 0.1939 0.2312 0.0 100.0
X Ray Diffraction 3.6437 4.0103 -- 140 2643 0.1901 0.21 0.0 100.0
X Ray Diffraction 4.0103 4.5903 -- 140 2662 0.1517 0.1927 0.0 100.0
X Ray Diffraction 4.5903 5.7823 -- 140 2661 0.1606 0.1868 0.0 100.0
X Ray Diffraction 5.7823 53.894 -- 143 2710 0.1568 0.1863 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.8571
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4964
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 110

Software

Software
Software Name Purpose
PHENIX refinement
XDS data reduction
XSCALE data scaling
PHASER phasing version: 2.8.1
PDB_EXTRACT data extraction version: 3.25