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Crystal Structure of the ER-alpha Ligand-binding Domain (L372S, L536S) in complex with DMERI-8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QXS pdbid 2QXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 298 20-25% PEG 3350, 200 mM MgCl2, 0.1 M Bis-Tris/Hepes/Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.087 α = 86.88 b = 58.816 β = 75.21 c = 93.709 γ = 63.4
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 PILATUS 6M 2018-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.0 SSRL BL12-2
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 1.78 90.39 54.3 0.997 9 3.8 49778
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 1.78 2.02 0.553
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 pdbid 2QXS 1.78 90.39 47320 2474 52.98 0.1989 0.1962 0.2047 0.2509 0.2522 RANDOM 35.832
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] 0.11 -0.02 -0.22 -0.02 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.723 r_dihedral_angle_4_deg 18.365 r_dihedral_angle_3_deg 15.29 r_dihedral_angle_1_deg 5.992 r_angle_refined_deg 1.382 r_angle_other_deg 1.196 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.723 r_dihedral_angle_4_deg 18.365 r_dihedral_angle_3_deg 15.29 r_dihedral_angle_1_deg 5.992 r_angle_refined_deg 1.382 r_angle_other_deg 1.196 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7803 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 130
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction AutoProcess data reduction