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Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with an Oxabicyclic diarylethylene Compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ERD PDB entry 3ERD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.02 39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.765 α = 90 b = 81.718 β = 109.9 c = 58.31 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 bent conical Si-mirror (Rh coating) 2004-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9734 APS 14-BM-C
Data Collection Overall ID # 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 2.7 20 97.8 0.113 0.113 14.8 3.5 13294 13294 17.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 98.7 0.546 0.546 3.47 3.4 1332
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3ERD 2.7 19.73 13275 13275 691 97.74 0.209 0.205 0.2032 0.291 0.2891 RANDOM 17.364
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.11 -0.56 4.93 -3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.287 r_dihedral_angle_4_deg 29.452 r_dihedral_angle_3_deg 20.918 r_dihedral_angle_1_deg 6.179 r_scangle_it 5.372 r_scbond_it 3.598 r_mcangle_it 2.444 r_angle_refined_deg 1.92 r_mcbond_it 1.665 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.287 r_dihedral_angle_4_deg 29.452 r_dihedral_angle_3_deg 20.918 r_dihedral_angle_1_deg 6.179 r_scangle_it 5.372 r_scbond_it 3.598 r_mcangle_it 2.444 r_angle_refined_deg 1.92 r_mcbond_it 1.665 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.268 r_symmetry_hbond_refined 0.243 r_chiral_restr 0.212 r_xyhbond_nbd_refined 0.17 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3845 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction MOLREP phasing