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Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with WAY-169916
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 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 39.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.806 α = 90 b = 82.029 β = 109.04 c = 58.517 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 1.72 15 95.4 0.046 0.046 27.9 4.7 48276 30.73
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 1.72 1.86 82.1 0.176 0.176 6.57 3.4 3762
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT PDB entry 3ERD 1.72 9.91 48124 48124 2446 91.58 0.18 0.178 0.221 0.2483 RANDOM 17.541
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] -0.05 -0.02 -0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.345 r_dihedral_angle_4_deg 23.794 r_dihedral_angle_3_deg 15.49 r_dihedral_angle_1_deg 8.04 r_scangle_it 3.65 r_scbond_it 2.504 r_mcangle_it 1.508 r_angle_refined_deg 1.489 r_angle_other_deg 0.993 r_mcbond_it 0.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.345 r_dihedral_angle_4_deg 23.794 r_dihedral_angle_3_deg 15.49 r_dihedral_angle_1_deg 8.04 r_scangle_it 3.65 r_scbond_it 2.504 r_mcangle_it 1.508 r_angle_refined_deg 1.489 r_angle_other_deg 0.993 r_mcbond_it 0.991 r_symmetry_vdw_refined 0.533 r_symmetry_hbond_refined 0.383 r_symmetry_vdw_other 0.334 r_mcbond_other 0.241 r_nbd_refined 0.238 r_nbd_other 0.211 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.183 r_chiral_restr 0.151 r_nbtor_other 0.112 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3816 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 48
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 PHASER phasing