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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% PPG400
Crystal Properties Matthews coefficient Solvent content 2.24 45.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.565 α = 90 b = 108.606 β = 90 c = 57.525 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 9M 2019-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.8 68.17 93.8 0.93 4.1 7.1 48490
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 0.54
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 68.17 45754 2430 93.36 0.19146 0.18923 0.2013 0.23459 0.2443 RANDOM 30.296
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] 0.49 -1 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.966 r_dihedral_angle_4_deg 20.236 r_dihedral_angle_3_deg 14.28 r_long_range_B_refined 7.361 r_long_range_B_other 7.242 r_dihedral_angle_1_deg 6.061 r_scangle_other 5.339 r_mcangle_other 3.703 r_mcangle_it 3.702 r_scbond_it 3.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.966 r_dihedral_angle_4_deg 20.236 r_dihedral_angle_3_deg 14.28 r_long_range_B_refined 7.361 r_long_range_B_other 7.242 r_dihedral_angle_1_deg 6.061 r_scangle_other 5.339 r_mcangle_other 3.703 r_mcangle_it 3.702 r_scbond_it 3.533 r_scbond_other 3.526 r_mcbond_it 2.679 r_mcbond_other 2.676 r_angle_refined_deg 1.86 r_angle_other_deg 1.059 r_chiral_restr 0.111 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 4298 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction SCALA data scaling PHASER phasing