X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details 100 mM HEPES, 200 mM MgCl2, 31% PEG400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.12 α = 90
b = 61.12 β = 90
c = 145.98 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M-F -- 2015-04-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.000 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
1.9 48.66 100.0 0.12 -- -- 19.3 -- 25730 -- -- 29.61
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)
1.9 1.94 100.0 1.853 -- 2.0 19.1 1596

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
FOURIER SYNTHESIS 1.9 48.66 -- 1.35 -- 25676 1251 99.98 -- 0.1653 0.1636 0.1979 Random selection
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 1.9 1.9761 -- 121 2667 0.242 0.3014 -- 100.0
X Ray Diffraction 1.9761 2.066 -- 134 2650 0.2145 0.244 -- 100.0
X Ray Diffraction 2.066 2.175 -- 152 2668 0.1898 0.2312 -- 100.0
X Ray Diffraction 2.175 2.3112 -- 133 2676 0.1749 0.2106 -- 100.0
X Ray Diffraction 2.3112 2.4897 -- 140 2675 0.1589 0.1881 -- 100.0
X Ray Diffraction 2.4897 2.7402 -- 128 2721 0.1644 0.1985 -- 100.0
X Ray Diffraction 2.7402 3.1367 -- 146 2721 0.1673 0.2212 -- 100.0
X Ray Diffraction 3.1367 3.9516 -- 157 2738 0.1486 0.1824 -- 100.0
X Ray Diffraction 3.9516 48.6756 -- 140 2909 0.1508 0.1747 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 40.8004
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.049
f_bond_d 0.018
f_angle_d 0.883
f_plane_restr 0.005
f_dihedral_angle_d 12.416
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2389
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 195

Software

Software
Software Name Purpose
Aimless data scaling version: 0.5.8
PHENIX refinement
PDB_EXTRACT data extraction version: 3.15
XDS data reduction
Coot model building