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x-ray structure of acyl-CoA thioesterase I, TesA, triple mutant M141L/Y145K/L146K in complex with octanoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TID
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 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.5 α = 90 b = 55 β = 104.9 c = 42 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 2016-07-19 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 0.97 50 97.8 0.06 0.006 11.8 4.1 102836
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 0.97 1.07 92.8 0.278 2.4 2.3
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 FOURIER SYNTHESIS THROUGHOUT 5tid 0.97 40.59 97699 5137 97.83 0.12276 0.12198 0.1213 0.13736 0.1356 RANDOM 16.085
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] 0.04 0.18 -0.02 -0.1
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 76.848 r_dihedral_angle_2_deg 36.083 r_sphericity_bonded 19.723 r_dihedral_angle_4_deg 17.684 r_dihedral_angle_3_deg 13.351 r_long_range_B_refined 9.682 r_long_range_B_other 9.682 r_rigid_bond_restr 7.68 r_scbond_it 7.085 r_scbond_other 7.085
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 76.848 r_dihedral_angle_2_deg 36.083 r_sphericity_bonded 19.723 r_dihedral_angle_4_deg 17.684 r_dihedral_angle_3_deg 13.351 r_long_range_B_refined 9.682 r_long_range_B_other 9.682 r_rigid_bond_restr 7.68 r_scbond_it 7.085 r_scbond_other 7.085 r_scangle_other 6.679 r_dihedral_angle_1_deg 6.024 r_mcangle_other 2.675 r_mcangle_it 2.661 r_mcbond_it 2.136 r_mcbond_other 2.028 r_angle_refined_deg 2.012 r_angle_other_deg 1.533 r_chiral_restr 0.138 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1440 Nucleic Acid Atoms Solvent Atoms 422 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing