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Human Estrogen Receptor beta Ligand-binding Domain in Complex with S-DPN
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 = 52.194 α = 90 b = 89.014 β = 90 c = 101.328 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 2019-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 1.54 46.443 99.6 0.998 18.7 11.6 69739
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 1.54 1.57 0.577
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 1.544 46.443 69667 3392 99.514 0.208 0.2063 0.2043 0.2375 0.2358 RANDOM 19.881
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] -0.187 0.17 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.464 r_dihedral_angle_3_deg 16.108 r_dihedral_angle_2_deg 12.634 r_lrange_it 6.161 r_lrange_other 6.16 r_dihedral_angle_1_deg 5.546 r_scangle_it 4.996 r_scangle_other 4.995 r_scbond_it 3.351 r_scbond_other 3.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.464 r_dihedral_angle_3_deg 16.108 r_dihedral_angle_2_deg 12.634 r_lrange_it 6.161 r_lrange_other 6.16 r_dihedral_angle_1_deg 5.546 r_scangle_it 4.996 r_scangle_other 4.995 r_scbond_it 3.351 r_scbond_other 3.35 r_mcangle_it 3.099 r_mcangle_other 3.099 r_mcbond_it 2.225 r_mcbond_other 2.225 r_angle_refined_deg 1.738 r_angle_other_deg 0.583 r_symmetry_nbd_refined 0.28 r_nbd_refined 0.246 r_nbd_other 0.238 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.175 r_symmetry_xyhbond_nbd_refined 0.174 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3543 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling MOLREP phasing