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X-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 5 in complex with octanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 20-25% PEG-5000, 100 mM homopipes, 3 mM octanoic acid
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.716 α = 90 b = 55.177 β = 105.18 c = 42.33 γ = 90
Symmetry Space Group P 1 21 1
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 Bruker Platinum 135 montel 2016-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.2 50 99.5 0.056 0.056 13.2 3.7 56148
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.3 97.3 0.302 3 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5TIC 1.2 40.85 53269 2879 99.4 0.15929 0.15832 0.1586 0.17746 0.1776 RANDOM 11.811
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] 0.1 -0.2 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.57 r_dihedral_angle_4_deg 17.042 r_dihedral_angle_3_deg 15.172 r_long_range_B_refined 6.622 r_long_range_B_other 6.204 r_dihedral_angle_1_deg 5.477 r_scangle_other 4.959 r_scbond_it 3.218 r_scbond_other 3.216 r_mcangle_other 1.892
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.57 r_dihedral_angle_4_deg 17.042 r_dihedral_angle_3_deg 15.172 r_long_range_B_refined 6.622 r_long_range_B_other 6.204 r_dihedral_angle_1_deg 5.477 r_scangle_other 4.959 r_scbond_it 3.218 r_scbond_other 3.216 r_mcangle_other 1.892 r_mcangle_it 1.887 r_angle_refined_deg 1.737 r_mcbond_it 1.269 r_mcbond_other 1.244 r_angle_other_deg 0.838 r_chiral_restr 0.118 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.001 r_bond_other_d 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 1410 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing