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Optimization of Orally Bioavailable Alkyl Amine Renin Inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D91 pdb entry 3D91
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 278 0.1M Tris-HCl pH=7.0-8.0, 0.2M (NH4)2SO4, 18-26%(w/v) PEG3350, 5mg/ml Renin, 1mM Inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.834 α = 90 b = 96.94 β = 90 c = 148.568 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 CCD ADSC QUANTUM 315 2005-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 0.9000 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.86 81.11 94 0.066 19.86 4.7 62269 62269
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.95 95.3 0.3194 3.69 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 3D91 1.9 50 62137 48486 2591 82.16 0.20334 0.20027 0.2018 0.26135 0.2624 RANDOM 28.111
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] -1.39 2.07 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.828 r_dihedral_angle_3_deg 16.337 r_dihedral_angle_4_deg 13.319 r_dihedral_angle_1_deg 8.015 r_scangle_it 4.692 r_scbond_it 3.2 r_angle_refined_deg 2.119 r_mcangle_it 2.03 r_mcbond_it 1.231 r_symmetry_hbond_refined 0.383
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.828 r_dihedral_angle_3_deg 16.337 r_dihedral_angle_4_deg 13.319 r_dihedral_angle_1_deg 8.015 r_scangle_it 4.692 r_scbond_it 3.2 r_angle_refined_deg 2.119 r_mcangle_it 2.03 r_mcbond_it 1.231 r_symmetry_hbond_refined 0.383 r_nbtor_refined 0.321 r_xyhbond_nbd_refined 0.271 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.229 r_chiral_restr 0.145 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5167 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 186
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling