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Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R)-3-(2-chloro-4-hydroxyphenyl)-2-(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 2.02 39.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.728 α = 90 b = 88.58 β = 90 c = 101.252 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 2019-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.08 46.06 97.5 0.995 5.6 6.4 28068
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.13 0.068
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 (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 2giu 2.08 46.06 28068 1387 97.5 0.2673 0.241 0.2497 0.307 0.3151 RANDOM 36.228
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] -1.03 1.74 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.624 r_dihedral_angle_3_deg 15.71 r_dihedral_angle_4_deg 14.304 r_dihedral_angle_1_deg 5.971 r_mcangle_it 4.856 r_mcbond_it 3.354 r_mcbond_other 3.348 r_angle_other_deg 2.368 r_angle_refined_deg 1.556 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.624 r_dihedral_angle_3_deg 15.71 r_dihedral_angle_4_deg 14.304 r_dihedral_angle_1_deg 5.971 r_mcangle_it 4.856 r_mcbond_it 3.354 r_mcbond_other 3.348 r_angle_other_deg 2.368 r_angle_refined_deg 1.556 r_chiral_restr 0.072 r_bond_other_d 0.036 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3427 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing