☰ Navigation Tabs
x-ray structure of acyl-CoA thioesterase I, TesA, mutant M141L/Y145K/L146K at pH 7.5 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 7.5 293 24-28% PEG-5000, 100 mM Hepes, 3 mM octanoic acid
Crystal Properties Matthews coefficient Solvent content 2.22 44.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.759 α = 90 b = 55.306 β = 104.91 c = 42.22 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 2016-07-24 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 1.15 50 98.2 0.045 0.045 11 2.3 62723
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 1.15 1.25 91.8 0.21 2.7 1.3
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 1.15 40.8 59641 3082 98.17 0.13074 0.12911 0.1293 0.16253 0.1627 RANDOM 12.293
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] -0.01 -0.15 -0.02 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.271 r_sphericity_free 21.684 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_4_deg 12.189 r_sphericity_bonded 8.633 r_rigid_bond_restr 7.135 r_dihedral_angle_1_deg 5.567 r_long_range_B_refined 3.757 r_scangle_other 3.149 r_long_range_B_other 3.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.271 r_sphericity_free 21.684 r_dihedral_angle_3_deg 12.333 r_dihedral_angle_4_deg 12.189 r_sphericity_bonded 8.633 r_rigid_bond_restr 7.135 r_dihedral_angle_1_deg 5.567 r_long_range_B_refined 3.757 r_scangle_other 3.149 r_long_range_B_other 3.051 r_scbond_it 2.981 r_scbond_other 2.979 r_angle_refined_deg 1.904 r_mcangle_it 1.527 r_mcangle_other 1.526 r_mcbond_other 1.306 r_mcbond_it 1.304 r_angle_other_deg 0.884 r_chiral_restr 0.124 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 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 1435 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing