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Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with an Oxabicyclic Derivative 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 8.5 298 0.1M Tris 8.5, 0.2M Magnesium Hexahydrate, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.987 α = 90 b = 84.002 β = 108.85 c = 58.724 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97946 SSRL BL11-1
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 10 89.4 0.062 0.062 18.65 4 31055 31055 28.72
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 2.07 92.2 0.156 0.156 10.65 4 3192
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 10 29429 30981 1552 89.07 0.216 0.214 0.2205 0.262 0.2721 RANDOM 17.465
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] -1.79 -0.35 2.89 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.149 r_dihedral_angle_4_deg 21.541 r_dihedral_angle_3_deg 17.053 r_dihedral_angle_1_deg 5.797 r_scangle_it 2.994 r_scbond_it 1.933 r_angle_refined_deg 1.546 r_mcangle_it 1.315 r_angle_other_deg 0.992 r_mcbond_it 0.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.149 r_dihedral_angle_4_deg 21.541 r_dihedral_angle_3_deg 17.053 r_dihedral_angle_1_deg 5.797 r_scangle_it 2.994 r_scbond_it 1.933 r_angle_refined_deg 1.546 r_mcangle_it 1.315 r_angle_other_deg 0.992 r_mcbond_it 0.838 r_symmetry_vdw_other 0.272 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.204 r_nbd_other 0.187 r_symmetry_hbond_refined 0.182 r_nbtor_refined 0.178 r_symmetry_vdw_refined 0.174 r_mcbond_other 0.171 r_nbtor_other 0.091 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3978 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 58
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling