5DUG

Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with a Sulfoxide-bridged Oxabicyclic Heptene Sulfonate (SOBHS)-2 analog phenyl (1S,2S,4S,7S)-5,6-bis(4-hydroxy-2-methylphenyl)-7-thiabicyclo[2.2.1]hept-5-ene-2-sulfonate 7-oxide


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 = 54.14 α = 90
b = 82.15 β = 110.87
c = 58.35 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 -- 2011-07-08
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
2.25 50 99.9 0.072 -- 27.175 3.8 -- 22491 -- -- --
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)
2.27 2.31 99.8 0.327 -- -- 3.8 1111

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 2.252 46.185 -- 0.0 -- 21741 1937 95.89 -- 0.1929 0.189 0.2331 --
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 2.2523 2.3087 -- 116 1051 0.234 0.3248 -- 73.0
X Ray Diffraction 2.3087 2.3711 -- 137 1388 0.2169 0.2646 -- 95.0
X Ray Diffraction 2.3711 2.4409 -- 127 1407 0.2079 0.2616 -- 95.0
X Ray Diffraction 2.4409 2.5196 -- 138 1432 0.1936 0.2329 -- 97.0
X Ray Diffraction 2.5196 2.6097 -- 139 1404 0.2031 0.2462 -- 97.0
X Ray Diffraction 2.6097 2.7142 -- 130 1426 0.2097 0.317 -- 96.0
X Ray Diffraction 2.7142 2.8377 -- 145 1409 0.2208 0.2859 -- 97.0
X Ray Diffraction 2.8377 2.9873 -- 145 1459 0.2045 0.2422 -- 98.0
X Ray Diffraction 2.9873 3.1744 -- 140 1459 0.2081 0.2719 -- 99.0
X Ray Diffraction 3.1744 3.4194 -- 142 1450 0.1914 0.2773 -- 98.0
X Ray Diffraction 3.4194 3.7634 -- 145 1447 0.1803 0.2068 -- 99.0
X Ray Diffraction 3.7634 4.3076 -- 146 1465 0.1586 0.2028 -- 99.0
X Ray Diffraction 4.3076 5.4258 -- 145 1494 0.1589 0.1827 -- 100.0
X Ray Diffraction 5.4258 46.1949 -- 142 1513 0.1958 0.215 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.7113
Anisotropic B[1][1] -1.1869
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.2935
Anisotropic B[2][2] 1.3436
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.1567
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.282
f_bond_d 0.004
f_dihedral_angle_d 14.815
f_plane_restr 0.007
f_chiral_restr 0.089
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3804
Nucleic Acid Atoms 0
Heterogen Atoms 68
Solvent Atoms 138

Software

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