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Crystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor TAM16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V3W PDB entry 5V3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING 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 43.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.627 α = 90 b = 108.762 β = 90 c = 56.735 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 CCD ADSC QUANTUM 315 2015-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 50 94.1 0.147 0.15 0.072 5.7 6.7 41704
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 1.9 1.93 86.5 0.907 0.501 0.782 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB entry 5V3W 1.98 34.584 1.35 36725 1861 93.26 0.1959 0.1936 0.2035 0.2386 0.2409 Random selection 36.5317
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.499 f_angle_d 1.085 f_chiral_restr 0.071 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4155 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 61
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction DENZO data reduction PHENIX phasing