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Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with bisphenol A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S9Q PDB ENTRY 1S9Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.05M HEPES, 0.75M sodium citrate, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.54 51.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.046 α = 90 b = 64.046 β = 90 c = 136.871 γ = 90
Symmetry Space Group P 41 21 2
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 RIGAKU JUPITER 210 2006-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.00 SPring-8 BL38B1
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 1.6 28.06 99.6 0.058 0.058 40.4 11.9 36414 36414
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 1.6 1.66 99.2 0.349 0.349 8.2 11.3 3729
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 (All) 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 1S9Q 1.6 28.06 36414 36414 1921 99.61 0.17071 0.17071 0.16934 0.1823 0.19666 0.2088 RANDOM 16.709
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.123 r_scangle_it 3.479 r_scbond_it 2.116 r_mcangle_it 1.336 r_angle_refined_deg 1.333 r_angle_other_deg 0.822 r_mcbond_it 0.714 r_symmetry_vdw_other 0.245 r_nbd_other 0.228 r_nbd_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.123 r_scangle_it 3.479 r_scbond_it 2.116 r_mcangle_it 1.336 r_angle_refined_deg 1.333 r_angle_other_deg 0.822 r_mcbond_it 0.714 r_symmetry_vdw_other 0.245 r_nbd_other 0.228 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.154 r_symmetry_vdw_refined 0.124 r_nbtor_other 0.085 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1806 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement BBS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing