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Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor X20404
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 0.1 M TRIS-HCL, 2.0-1.8 M AMMONIUM
SULFATE, 2%-5% V/V PPG P400
Crystal Properties Matthews coefficient Solvent content 2.18 43.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.942 α = 90 b = 87.592 β = 90 c = 109.382 γ = 90
Symmetry Space Group P 2 21 21
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 PILATUS 6M 2020-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00003 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.1 48.37 92.1 0.088 0.052 0.997 10.1 3.3 30403
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 68 0.648 0.54 0.633 1.8 2.6
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 2.1 48.37 28866 1511 91.4 0.18711 0.18454 0.1963 0.23764 0.2515 RANDOM 37.196
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] 0.25 -0.39 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 6.783 r_long_range_B_refined 6.725 r_long_range_B_other 6.68 r_scangle_other 3.933 r_mcangle_other 3.189 r_mcangle_it 3.188 r_scbond_it 2.846 r_scbond_other 2.546 r_mcbond_it 2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 6.783 r_long_range_B_refined 6.725 r_long_range_B_other 6.68 r_scangle_other 3.933 r_mcangle_other 3.189 r_mcangle_it 3.188 r_scbond_it 2.846 r_scbond_other 2.546 r_mcbond_it 2.06 r_mcbond_other 2.058 r_angle_refined_deg 1.092 r_angle_other_deg 0.4 r_chiral_restr 0.053 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4294 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 98
Software Software Software Name Purpose PDB-REDO refinement XDS data reduction Aimless data scaling MOLREP phasing