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Identification of Spirooxindole and Dibenzoxazepine Motifs as Potent Mineralocorticoid Receptor Antagonists
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A3I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 1uL of protein complex at 8-10mg protein/ml is mixed with an equal volume of reservoir solution composed of 100mM Tris-HCl pH=8.0, 200mM NaCl, 5% (v/v) glycerol, 16%(w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.501 α = 90 b = 121.501 β = 90 c = 44.406 γ = 120
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 ADSC QUANTUM 315r Cryogenically-cooled monochromator+vertical focusing mirror 2011-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.5 44.41 99.97 0.165 18.5 10.9 25409 24098 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.499 2.564 99.79 0.95 2.6 8.3
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 2A3I 2.5 44.41 24098 1292 99.97 0.17427 0.16998 0.1869 0.25571 0.2543 RANDOM 50.713
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] -0.02 -0.01 -0.02 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.887 r_dihedral_angle_3_deg 18.092 r_dihedral_angle_4_deg 16.646 r_long_range_B_refined 10.362 r_dihedral_angle_1_deg 5.583 r_mcangle_it 5.167 r_scbond_it 4.865 r_mcbond_it 3.49 r_angle_refined_deg 1.609 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.887 r_dihedral_angle_3_deg 18.092 r_dihedral_angle_4_deg 16.646 r_long_range_B_refined 10.362 r_dihedral_angle_1_deg 5.583 r_mcangle_it 5.167 r_scbond_it 4.865 r_mcbond_it 3.49 r_angle_refined_deg 1.609 r_chiral_restr 0.105 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5744 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing