X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 292.0
Details 1 uL + 1uL drop with 500 uL reservoir solution: 100 mM Tris-MES pH 6.5, 75 mM K-Citrate, 24-28% w/w PEG550 MME and 10% (v/v) glycerol; protein buffer: 10 mM Tris-MES pH 6.0, 100 mM KCl, 10% (v/v) glycerol, 40 mM n-octyl-beta-D-glucoside

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.57 α = 90
b = 92.08 β = 95.18
c = 92.47 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2014-08-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24

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
2.5 49.3 99.1 -- -- -- 6.9 -- 46789 -- -- --
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)
2.5 2.59 98.5 -- -- -- 6.8 --

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 2.5 46.046 -- 1.35 -- 46789 1000 98.97 -- 0.2234 0.223 0.2447 --
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 2.5001 2.6319 -- 138 6434 0.375 0.37 -- 98.0
X Ray Diffraction 2.6319 2.7967 -- 141 6497 0.3158 0.3353 -- 99.0
X Ray Diffraction 2.7967 3.0126 -- 141 6466 0.2716 0.2959 -- 99.0
X Ray Diffraction 3.0126 3.3157 -- 145 6541 0.2491 0.3104 -- 99.0
X Ray Diffraction 3.3157 3.7953 -- 143 6544 0.2154 0.2516 -- 99.0
X Ray Diffraction 3.7953 4.7809 -- 145 6616 0.1999 0.2347 -- 100.0
X Ray Diffraction 4.7809 46.0542 -- 147 6691 0.1993 0.204 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_angle_d 0.621
f_dihedral_angle_d 15.06
f_chiral_restr 0.04
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7971
Nucleic Acid Atoms 0
Heterogen Atoms 209
Solvent Atoms 44

Software

Software
Software Name Purpose
PHENIX refinement version: (dev_2283: ???)
XDS data reduction
XSCALE data scaling
PHENIX phasing