5DP0

Crystal Structure of the ER-alpha Ligand-binding Domain in complex with a 4-fluorophenylamino-substituted triaryl-ethylene derivative 4,4'-(2-{3-[(4-fluorophenyl)amino]phenyl}ethene-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 = 56.03 α = 90
b = 83.08 β = 111.06
c = 58.88 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 -- 2011-03-21
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 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
2.38 50 100.0 0.053 -- 30.413 3.8 -- 20228 -- -- --
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)
2.38 2.42 100.0 0.592 -- -- 3.8 1034

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 2.382 41.11 -- 0.0 -- 17880 1779 88.31 -- 0.1937 0.1888 0.2379 --
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 2.3824 2.4468 -- 48 518 0.2158 0.2551 -- 36.0
X Ray Diffraction 2.4468 2.5188 -- 110 864 0.2223 0.2537 -- 63.0
X Ray Diffraction 2.5188 2.6001 -- 122 1150 0.2404 0.3626 -- 83.0
X Ray Diffraction 2.6001 2.693 -- 151 1245 0.2487 0.2843 -- 90.0
X Ray Diffraction 2.693 2.8008 -- 145 1287 0.2322 0.3183 -- 92.0
X Ray Diffraction 2.8008 2.9282 -- 144 1335 0.2312 0.2978 -- 96.0
X Ray Diffraction 2.9282 3.0825 -- 145 1345 0.2184 0.272 -- 95.0
X Ray Diffraction 3.0825 3.2756 -- 147 1352 0.2161 0.2635 -- 97.0
X Ray Diffraction 3.2756 3.5284 -- 148 1379 0.1942 0.2406 -- 99.0
X Ray Diffraction 3.5284 3.8832 -- 142 1387 0.1689 0.2495 -- 99.0
X Ray Diffraction 3.8832 4.4446 -- 161 1393 0.1496 0.1923 -- 99.0
X Ray Diffraction 4.4446 5.5974 -- 159 1416 0.156 0.1898 -- 100.0
X Ray Diffraction 5.5974 41.1158 -- 157 1430 0.1801 0.2052 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 49.7494
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.004
f_chiral_restr 0.028
f_plane_restr 0.003
f_angle_d 0.756
f_dihedral_angle_d 14.446
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3708
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 95

Software

Software
Software Name Purpose
PHENIX refinement version: 1.8.2_1309
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing