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Synthesis, Biological Activity, and X-Ray Crystal Structural Analysis of Diaryl Ether Inhibitors of Malarial Enoyl ACP Reductase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 2.35 M (NH4)2SO4, 100 sodium acetate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.861 α = 90 b = 130.861 β = 90 c = 82.687 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE RIGAKU RAXIS IV 2004-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 33.8 25282 23997
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-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 1NHD 2.5 33.77 23997 1285 99.28 0.19655 0.19655 0.19343 0.196 0.25493 0.1939 RANDOM 37.069
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.249 r_dihedral_angle_4_deg 19.701 r_dihedral_angle_3_deg 18.427 r_scangle_it 7.718 r_scbond_it 5.888 r_dihedral_angle_1_deg 5.67 r_mcangle_it 4.249 r_mcbond_it 2.819 r_angle_refined_deg 1.517 r_nbtor_refined 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.249 r_dihedral_angle_4_deg 19.701 r_dihedral_angle_3_deg 18.427 r_scangle_it 7.718 r_scbond_it 5.888 r_dihedral_angle_1_deg 5.67 r_mcangle_it 4.249 r_mcbond_it 2.819 r_angle_refined_deg 1.517 r_nbtor_refined 0.336 r_symmetry_vdw_refined 0.271 r_nbd_refined 0.26 r_symmetry_hbond_refined 0.243 r_xyhbond_nbd_refined 0.202 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 4576 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement AMoRE phasing