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New 5-Benzylidenethiazolidine-4-one Inhibitors of Bacterial MurD Ligase: Design, Synthesis, Crystal Structures, and Biological Evaluation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UAG PDB ENTRY 1UAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 6.0 MG/ML MURD, 20 MM HEPES PH 7.4, 200MM NACL, 5MM DITHIOTHREITOL, 0.05% (W/V) NAN3, 0.1M HEPES PH 7.5, 1.9 M AMMONIUM SULPHATE, 7% (W/V) PEG 400, 50 MM NACL
Crystal Properties Matthews coefficient Solvent content 2.99 58.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.326 α = 90 b = 65.326 β = 90 c = 134.707 γ = 90
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 CCD 2010-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.85 46.89 84.3 0.04 33.79 5 45564 3 40.14
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 1.85 1.96 55.3 0.45 3.06 3.4
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 PDB ENTRY 1UAG 1.85 46.89 40963 4601 100 0.21211 0.208 0.2094 0.24852 0.2512 RANDOM 38.663
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] 0.8 0.8 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.568 r_dihedral_angle_4_deg 16.831 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_1_deg 7.274 r_scangle_it 6.098 r_scbond_it 4.156 r_mcangle_it 2.508 r_mcbond_it 1.647 r_angle_refined_deg 1.378 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.568 r_dihedral_angle_4_deg 16.831 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_1_deg 7.274 r_scangle_it 6.098 r_scbond_it 4.156 r_mcangle_it 2.508 r_mcbond_it 1.647 r_angle_refined_deg 1.378 r_chiral_restr 0.109 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_other r_long_range_B_refined 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 3276 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing