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Second-generation sulfonamide inhibitors of MurD: Activity optimisation with conformationally rigid analogues of D-glutamic acid
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 7.5 1.9M (NH4)2SO4,7% PEG 400, 50MM NACL, 100MM HEPES, PH 7.5
Crystal Properties Matthews coefficient Solvent content 3.05 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.659 α = 90 b = 65.659 β = 90 c = 135.642 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 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 1.49 46.43 91.2 0.04 29.8 6 91001 3 26.667
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 1.49 1.58 69.6 0.49 3.09 4.2
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 46.43 81535 9058 100 0.17608 0.17353 0.1739 0.19924 0.1997 RANDOM 23.923
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] 0.08 0.08 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.299 r_dihedral_angle_4_deg 14.799 r_dihedral_angle_3_deg 12.592 r_dihedral_angle_1_deg 6.178 r_scangle_it 5.456 r_scbond_it 3.598 r_mcangle_it 2.414 r_mcbond_it 1.622 r_angle_refined_deg 1.558 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.299 r_dihedral_angle_4_deg 14.799 r_dihedral_angle_3_deg 12.592 r_dihedral_angle_1_deg 6.178 r_scangle_it 5.456 r_scbond_it 3.598 r_mcangle_it 2.414 r_mcbond_it 1.622 r_angle_refined_deg 1.558 r_chiral_restr 0.13 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 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 487 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing