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Discovery of Novel 5-Benzylidenerhodanine- and 5-Benzylidene- thiazolidine-2,4-dione Inhibitors of MurD Ligase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UAG PDB ENTRY 3UAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 1.8 M (NH4)2SO4, 7% PEG 400, 100 MM NACL, 100MM HEPES, PH 7.5
Crystal Properties Matthews coefficient Solvent content 3.1 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.091 α = 90 b = 66.091 β = 90 c = 135.781 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 2009-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.46 47.36 86.2 0.04 29 5.2 93804 3 24.226
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 1.46 1.55 52 0.41 3 2.6
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 3UAG 1.46 47.36 89100 4707 100 0.1868 0.18525 0.2042 0.21672 0.2374 RANDOM 13.805
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_scangle_it 5.038 r_scbond_it 3.489 r_mcangle_it 2.286 r_mcbond_it 1.532 r_bond_refined_d r_bond_other_d r_angle_refined_deg r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.038 r_scbond_it 3.489 r_mcangle_it 2.286 r_mcbond_it 1.532 r_bond_refined_d r_bond_other_d r_angle_refined_deg r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined 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 3304 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing