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Structure-based design of a new series of D-glutamic acid-based inhibitors of bacterial MurD ligase
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 3.02 59.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.544 α = 90 b = 65.544 β = 90 c = 134.959 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 QUANTUM 315r 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 1.49 46.35 87.8 0.03 34.43 5.2 88810 3 26.405
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 1.49 1.58 60.4 0.48 3.11 3.6
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 1UAG 1.49 46.35 79927 8882 100 0.1814 0.17892 0.1807 0.20359 0.2058 RANDOM 24.724
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] 0.28 0.28 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.921 r_dihedral_angle_4_deg 15.427 r_dihedral_angle_3_deg 12.494 r_dihedral_angle_1_deg 6.541 r_scangle_it 6.099 r_scbond_it 3.876 r_mcangle_it 2.529 r_mcbond_it 1.62 r_angle_refined_deg 1.477 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.921 r_dihedral_angle_4_deg 15.427 r_dihedral_angle_3_deg 12.494 r_dihedral_angle_1_deg 6.541 r_scangle_it 6.099 r_scbond_it 3.876 r_mcangle_it 2.529 r_mcbond_it 1.62 r_angle_refined_deg 1.477 r_chiral_restr 0.118 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 3278 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing