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Synthesis, Biological Activity, and X-Ray Crystal Structural Analysis of Diaryl Ether Inhibitors of Malarial Enoyl ACP Reductase. Part 1:4'-Substituted Triclosan Derivatives
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, pH 5.60
Crystal Properties Matthews coefficient Solvent content 2.7 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.035 α = 90 b = 131.035 β = 90 c = 82.946 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 MACSCIENCE OSMIC 2005-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 2.992 29.683 15087
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 1nhd 2.992 29.683 14292 758 99.8 0.191 0.188 0.1881 0.263 0.264 RANDOM 29.7
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] 0.52 0.52 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.116 r_dihedral_angle_3_deg 21.099 r_dihedral_angle_4_deg 18.54 r_scangle_it 6.332 r_dihedral_angle_1_deg 5.867 r_scbond_it 4.616 r_mcangle_it 3.847 r_mcbond_it 2.376 r_angle_refined_deg 1.477 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.116 r_dihedral_angle_3_deg 21.099 r_dihedral_angle_4_deg 18.54 r_scangle_it 6.332 r_dihedral_angle_1_deg 5.867 r_scbond_it 4.616 r_mcangle_it 3.847 r_mcbond_it 2.376 r_angle_refined_deg 1.477 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.227 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.102 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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 4634 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 126
Software Software Software Name Purpose XDIP data collection DENZO data reduction SCALEPACK data scaling REFMAC refinement XDIP data reduction