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Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor X20348
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 2.81 56.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.862 α = 90 b = 96.623 β = 90 c = 130.973 γ = 90
Symmetry Space Group P 21 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 EIGER X 16M 2021-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03320 APS 23-ID-B
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 2.35 48.36 85.8 0.174 0.098 0.986 5.3 3.4 25227
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 2.35 2.43 1.097 0.604 0.396 1.4 3.4
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 2.35 48.36 23988 1217 84.63 0.19903 0.19613 0.2087 0.25633 0.2571 RANDOM 49.033
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.999 r_dihedral_angle_1_deg 8.234 r_long_range_B_other 7.072 r_long_range_B_refined 7.071 r_scangle_other 5.167 r_mcangle_it 3.639 r_mcangle_other 3.639 r_scbond_it 3.434 r_scbond_other 3.313 r_mcbond_it 2.286
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.999 r_dihedral_angle_1_deg 8.234 r_long_range_B_other 7.072 r_long_range_B_refined 7.071 r_scangle_other 5.167 r_mcangle_it 3.639 r_mcangle_other 3.639 r_scbond_it 3.434 r_scbond_other 3.313 r_mcbond_it 2.286 r_mcbond_other 2.281 r_angle_refined_deg 1.592 r_angle_other_deg 0.574 r_chiral_restr 0.074 r_bond_refined_d 0.018 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4356 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 146
Software Software Software Name Purpose PDB-REDO refinement XDS data reduction Aimless data scaling MOLREP phasing