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Crystal Structure of the ER-alpha Ligand-binding Domain (L372S, L536S) in complex with DMERI-25
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 2.13 42.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.573 α = 86.7 b = 58.812 β = 75.09 c = 92.857 γ = 62.91
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 RAYONIX MX300-HS 2017-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.7 89.52 86.2 0.984 7.8 7.7 62849
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 1.7 1.9 0.526
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 1.7 89.52 59734 3121 58.87 0.2164 0.2145 0.2246 0.2517 0.2556 RANDOM 39.87
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] -0.17 -0.06 0.11 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.551 r_dihedral_angle_4_deg 18.49 r_dihedral_angle_3_deg 15.397 r_dihedral_angle_1_deg 6.574 r_angle_refined_deg 1.431 r_angle_other_deg 1.146 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.551 r_dihedral_angle_4_deg 18.49 r_dihedral_angle_3_deg 15.397 r_dihedral_angle_1_deg 6.574 r_angle_refined_deg 1.431 r_angle_other_deg 1.146 r_chiral_restr 0.09 r_bond_refined_d 0.011 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 7417 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction AutoProcess data reduction