5DKG

Crystal Structure of the ER-alpha Ligand-binding Domain in complex with a t-butyl-substituted, methyl, triaryl-ethylene derivative 4,4'-[2-(4-tert-butylphenyl)prop-1-ene-1,1-diyl]diphenol


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.3
Temperature 294.0
Details 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.34 α = 90
b = 82.08 β = 110.83
c = 58.62 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 PILATUS 6M -- 2012-07-27
Diffraction Radiation
Monochromator Protocol
Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 1.000 SSRL BL11-1

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
2.15 50 98.7 0.06 -- 22.735 6.9 -- 26939 -- -- --
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)
2.15 2.19 94.2 0.616 -- -- 6.1 1277

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
-- 2.15 45.57 -- 0.0 -- 25474 1878 93.31 -- 0.1963 0.1935 0.2325 --
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 2.1478 2.2058 -- 116 1543 0.2593 0.3212 -- 80.0
X Ray Diffraction 2.2058 2.2707 -- 144 1620 0.2647 0.288 -- 84.0
X Ray Diffraction 2.2707 2.344 -- 132 1726 0.2321 0.3015 -- 88.0
X Ray Diffraction 2.344 2.4278 -- 139 1769 0.2381 0.2966 -- 92.0
X Ray Diffraction 2.4278 2.525 -- 153 1790 0.2133 0.2411 -- 93.0
X Ray Diffraction 2.525 2.6399 -- 147 1846 0.2199 0.2672 -- 95.0
X Ray Diffraction 2.6399 2.7791 -- 139 1816 0.2135 0.2545 -- 94.0
X Ray Diffraction 2.7791 2.9532 -- 144 1865 0.2248 0.2884 -- 95.0
X Ray Diffraction 2.9532 3.1811 -- 154 1885 0.2125 0.2502 -- 98.0
X Ray Diffraction 3.1811 3.5012 -- 151 1940 0.1991 0.2484 -- 99.0
X Ray Diffraction 3.5012 4.0075 -- 152 1915 0.1688 0.2129 -- 98.0
X Ray Diffraction 4.0075 5.048 -- 154 1919 0.1552 0.1782 -- 98.0
X Ray Diffraction 5.048 45.5806 -- 153 1962 0.1796 0.2116 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.9108
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.003
f_dihedral_angle_d 14.297
f_chiral_restr 0.026
f_angle_d 0.683
f_plane_restr 0.002
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3848
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 189

Software

Software
Software Name Purpose
PHENIX refinement
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data reduction
PHENIX phasing