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Human Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-2-(2-chloro-4-hydroxyphenyl)-3-(4-hydroxyphenyl)propanenitrile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GIU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate
Crystal Properties Matthews coefficient Solvent content 2.04 39.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.436 α = 90 b = 89.226 β = 90 c = 101.532 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.16 46.633 99.3 0.451 0.537 0.288 0.937 4.4 5.9 25917
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.23 2.186 2.664 1.499 0.623 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2giu 2.164 46.633 25840 1294 98.955 0.264 0.2614 0.2663 0.3178 0.3269 RANDOM 26.142
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] 3.579 -9.383 5.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.882 r_dihedral_angle_3_deg 16.102 r_dihedral_angle_4_deg 15.571 r_dihedral_angle_1_deg 6.291 r_lrange_it 5.798 r_lrange_other 5.798 r_scangle_it 3.937 r_scangle_other 3.936 r_mcangle_it 3.581 r_mcangle_other 3.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.882 r_dihedral_angle_3_deg 16.102 r_dihedral_angle_4_deg 15.571 r_dihedral_angle_1_deg 6.291 r_lrange_it 5.798 r_lrange_other 5.798 r_scangle_it 3.937 r_scangle_other 3.936 r_mcangle_it 3.581 r_mcangle_other 3.581 r_scbond_it 2.432 r_scbond_other 2.432 r_mcbond_it 2.245 r_mcbond_other 2.244 r_angle_refined_deg 1.555 r_angle_other_deg 1.289 r_symmetry_xyhbond_nbd_refined 0.501 r_symmetry_nbd_refined 0.293 r_nbd_other 0.263 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.183 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.16 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3530 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing