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Identification and optimisation of novel inhibitors of the Polyketide synthetase 13 thioesterase domain with antitubercular activity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 1.65M AmSO4, 0.1M Tris, pH 8.5, 3% PPG 400
Crystal Properties Matthews coefficient Solvent content 2.19 43.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.273 α = 90 b = 110.247 β = 90 c = 57.862 γ = 90
Symmetry Space Group P 21 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 100 PIXEL DECTRIS PILATUS3 6M 2017-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.968 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.8 68.91 97.1 0.096 0.11 0.999 12.6 7.1 51471
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 99.9 0.625 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 68.91 48824 2565 96.8 0.18805 0.18611 0.1978 0.2242 0.2341 RANDOM 30.426
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] -0.03 -0.72 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.569 r_dihedral_angle_4_deg 22.902 r_dihedral_angle_3_deg 15.924 r_long_range_B_refined 6.937 r_long_range_B_other 6.929 r_dihedral_angle_1_deg 6.33 r_scangle_other 5.463 r_mcangle_it 3.785 r_mcangle_other 3.784 r_scbond_it 3.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.569 r_dihedral_angle_4_deg 22.902 r_dihedral_angle_3_deg 15.924 r_long_range_B_refined 6.937 r_long_range_B_other 6.929 r_dihedral_angle_1_deg 6.33 r_scangle_other 5.463 r_mcangle_it 3.785 r_mcangle_other 3.784 r_scbond_it 3.726 r_scbond_other 3.725 r_mcbond_it 2.727 r_mcbond_other 2.726 r_angle_refined_deg 1.808 r_angle_other_deg 1.097 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4290 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing