X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 35% (v/v) glycerol ethoxylate, 90 mM sodium malonate, pH7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.78 α = 90
b = 60.78 β = 90
c = 167.22 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M-F -- 2018-07-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.00000 SLS X06DA

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 44.55 100.0 -- 0.128 -- 19.7 -- 25042 -- -- 43.1
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)
2.0 2.12 99.9 -- 2.901 1.11 20.6 --

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 2.001 44.546 -- 1.34 -- 25042 1265 99.96 -- 0.2074 0.2057 0.2404 --
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 2.0007 2.0808 -- 146 2583 0.344 0.3343 -- 100.0
X Ray Diffraction 2.0808 2.1755 -- 139 2607 0.2998 0.3201 -- 100.0
X Ray Diffraction 2.1755 2.2902 -- 135 2588 0.3006 0.3048 -- 100.0
X Ray Diffraction 2.2902 2.4337 -- 138 2621 0.2579 0.2953 -- 100.0
X Ray Diffraction 2.4337 2.6216 -- 138 2597 0.246 0.2731 -- 100.0
X Ray Diffraction 2.6216 2.8854 -- 138 2624 0.2286 0.2798 -- 100.0
X Ray Diffraction 2.8854 3.3028 -- 138 2645 0.2207 0.2732 -- 100.0
X Ray Diffraction 3.3028 4.1607 -- 142 2674 0.1757 0.1837 -- 100.0
X Ray Diffraction 4.1607 44.557 -- 151 2838 0.1699 0.219 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.004
f_plane_restr 0.003
f_dihedral_angle_d 21.923
f_angle_d 0.639
f_chiral_restr 0.047
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2832
Nucleic Acid Atoms 77
Heterogen Atoms 2
Solvent Atoms 99

Software

Software
Software Name Purpose
PHENIX refinement version: (1.14_3211: ???)
XDS data reduction
Coot model building
PHASER phasing
XSCALE data scaling