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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 0.1M Tris-HCl pH 8.5, 1.8 M Ammonium sulfate, 3% v/v PPG400
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.45 α = 90 b = 109.846 β = 90 c = 57.59 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 EIGER2 XE 16M 2018-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.709 88.46 92 0.995 12.6 11.6 56541
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 1.709 1.77 0.764
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 1.71 88.45 53377 2738 91.28 0.19742 0.19531 0.2069 0.23869 0.2473 RANDOM 33.171
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] -0.57 -0.62 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.537 r_dihedral_angle_4_deg 20.608 r_dihedral_angle_3_deg 14.37 r_long_range_B_refined 7.564 r_long_range_B_other 7.564 r_dihedral_angle_1_deg 6.239 r_scangle_other 5.945 r_mcangle_it 4.297 r_mcangle_other 4.297 r_scbond_it 3.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.537 r_dihedral_angle_4_deg 20.608 r_dihedral_angle_3_deg 14.37 r_long_range_B_refined 7.564 r_long_range_B_other 7.564 r_dihedral_angle_1_deg 6.239 r_scangle_other 5.945 r_mcangle_it 4.297 r_mcangle_other 4.297 r_scbond_it 3.988 r_scbond_other 3.987 r_mcbond_it 3.066 r_mcbond_other 3.064 r_angle_refined_deg 1.973 r_angle_other_deg 1.103 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 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 4321 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing