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Crystal structure of the putative tol-pal system-associated acyl-CoA thioesterase from Pseudomonas aeruginosa PAO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M Succinic Acid pH 7.0, 15 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.994 α = 90 b = 62.279 β = 112.52 c = 52.792 γ = 90
Symmetry Space Group C 1 2 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 MARMOSAIC 300 mm CCD 2016-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 51.31 91.5 0.101 0.049 13.9 4 21234 -3
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 57.5 0.468 0.305 0.82 2.1 2.4
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 1S5U 1.9 51.31 17785 952 80.75 0.22315 0.21991 0.2253 0.28308 0.2889 RANDOM 32.493
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] -0.66 -0.1 -0.35 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_long_range_B_other 17.744 r_long_range_B_refined 17.74 r_dihedral_angle_4_deg 15.295 r_dihedral_angle_3_deg 15.006 r_scangle_other 14.731 r_scbond_it 11.585 r_scbond_other 11.583 r_mcangle_it 11.462 r_mcangle_other 11.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.876 r_long_range_B_other 17.744 r_long_range_B_refined 17.74 r_dihedral_angle_4_deg 15.295 r_dihedral_angle_3_deg 15.006 r_scangle_other 14.731 r_scbond_it 11.585 r_scbond_other 11.583 r_mcangle_it 11.462 r_mcangle_other 11.458 r_mcbond_it 8.708 r_mcbond_other 8.706 r_dihedral_angle_1_deg 6.811 r_angle_refined_deg 1.649 r_angle_other_deg 1.021 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2177 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing