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Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed to an Ether Estradiol 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 2.09 41.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.171 α = 90 b = 83.708 β = 108.45 c = 56.007 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 SBC-3 mirrors 2004-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97945 APS 19-BM
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 2.15 50 98.7 0.118 0.118 4.1 3.7 28301 28301 20.43
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 2.15 2.23 95.7 0.395 0.395 1.8 3.1 2736
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 2.15 20 28251 28251 1431 96.93 0.194 0.192 0.1937 0.24 0.2429 RANDOM 16.469
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] 0.12 -0.07 -0.07 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.744 r_dihedral_angle_3_deg 16.386 r_dihedral_angle_4_deg 15.846 r_dihedral_angle_1_deg 4.853 r_scangle_it 2.747 r_scbond_it 1.931 r_mcangle_it 1.471 r_angle_refined_deg 1.149 r_mcbond_it 0.986 r_angle_other_deg 0.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.744 r_dihedral_angle_3_deg 16.386 r_dihedral_angle_4_deg 15.846 r_dihedral_angle_1_deg 4.853 r_scangle_it 2.747 r_scbond_it 1.931 r_mcangle_it 1.471 r_angle_refined_deg 1.149 r_mcbond_it 0.986 r_angle_other_deg 0.914 r_symmetry_vdw_other 0.336 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.209 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.19 r_symmetry_hbond_refined 0.179 r_nbtor_refined 0.174 r_mcbond_other 0.173 r_nbtor_other 0.088 r_chiral_restr 0.071 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3978 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 46
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