5U2B

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the phenylamino-substituted estrogen, (8R,9S,13S,14S,17S)-13-methyl-17-(phenylamino)-7,8,9,11,12,13,14,15,16,17-decahydro-6H-cyclopenta[a]phenanthren-3-ol, without a coactivator peptide


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 = 60.58 α = 83.11
b = 64.44 β = 75.2
c = 135.41 γ = 61.99
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-12-18
Diffraction Radiation
Monochromator Protocol
Double crystal cryo-cooled Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.033 APS 23-ID-B

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
2.22 34.62 98.0 0.044 -- -- 2.0 -- 84041 -- -- --
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)
2.22 2.26 96.9 0.396 -- -- 2.0 --

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 2.22 34.63 -- 0.0 -- 84041 2047 97.8 -- 0.217 0.201 0.229 --
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 2.2234 2.279 -- 140 5546 0.3737 0.4142 -- 91.0
X Ray Diffraction 2.279 2.3406 -- 141 5843 0.3402 0.42 -- 95.0
X Ray Diffraction 2.3406 2.4094 -- 142 5821 0.3285 0.3325 -- 95.0
X Ray Diffraction 2.4094 2.4872 -- 142 5838 0.3096 0.351 -- 95.0
X Ray Diffraction 2.4872 2.576 -- 140 5863 0.2848 0.3732 -- 96.0
X Ray Diffraction 2.576 2.6791 -- 138 5907 0.2683 0.3022 -- 96.0
X Ray Diffraction 2.6791 2.8009 -- 150 5857 0.2564 0.2899 -- 96.0
X Ray Diffraction 2.8009 2.9484 -- 141 5845 0.2369 0.2981 -- 96.0
X Ray Diffraction 2.9484 3.1329 -- 136 5899 0.2233 0.2747 -- 96.0
X Ray Diffraction 3.1329 3.3745 -- 143 5937 0.2099 0.2027 -- 96.0
X Ray Diffraction 3.3745 3.7134 -- 147 5865 0.1883 0.1933 -- 96.0
X Ray Diffraction 3.7134 4.2492 -- 149 5940 0.167 0.2257 -- 96.0
X Ray Diffraction 4.2492 5.3477 -- 146 5960 0.1609 0.171 -- 97.0
X Ray Diffraction 5.3477 28.4482 -- 145 5899 0.1901 0.2484 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.95
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.002
f_dihedral_angle_d 17.813
f_angle_d 0.518
f_plane_restr 0.003
f_chiral_restr 0.033
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10767
Nucleic Acid Atoms 0
Heterogen Atoms 133
Solvent Atoms 700

Software

Software
Software Name Purpose
PHENIX refinement version: 1.10.1_2155
HKL-2000 data scaling
PDB_EXTRACT data extraction version: 3.20
HKL-2000 data reduction
PHENIX phasing
DENZO data reduction
SCALEPACK data scaling