X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.7
Temperature 293.0
Details MES, PEG 8000, NaOAc

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 115.69 α = 90
b = 115.69 β = 90
c = 119.8 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2014-05-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.0332 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
2.75 50 99.8 0.078 -- -- 7.1 -- 21704 -- -- 58.35
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)
2.75 2.92 99.1 0.568 -- 3.1 -- --

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 2.75 47.498 -- -- -- 21700 1085 99.83 -- 0.2083 0.2058 0.257 --
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 2.75 2.8751 -- 132 2495 0.2898 0.3763 -- 99.0
X Ray Diffraction 2.8751 3.0267 -- 132 2538 0.2677 0.3756 -- 100.0
X Ray Diffraction 3.0267 3.2163 -- 134 2533 0.2474 0.2991 -- 100.0
X Ray Diffraction 3.2163 3.4645 -- 133 2538 0.2343 0.2954 -- 100.0
X Ray Diffraction 3.4645 3.813 -- 135 2561 0.2027 0.2629 -- 100.0
X Ray Diffraction 3.813 4.3645 -- 136 2575 0.182 0.2368 -- 100.0
X Ray Diffraction 4.3645 5.4975 -- 138 2622 0.1704 0.2178 -- 100.0
X Ray Diffraction 5.4975 47.505 -- 145 2753 0.2001 0.227 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 64.4831
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.005
f_chiral_restr 0.04
f_dihedral_angle_d 16.37
f_plane_restr 0.005
f_angle_d 1.031
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5129
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 48

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling version: 2.5.2
PDB_EXTRACT data extraction version: 3.14
PHENIX refinement version: (phenix.refine: 1.9_1690)
PHASER phasing
XSCALE data reduction