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X-ray structure of wild-type E. coli Acyl-CoA thioesterase I at pH 5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 22-26% PEG-5000, 100 mM homopipesa
Crystal Properties Matthews coefficient Solvent content 2.19 43.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.922 α = 90 b = 82.124 β = 90.44 c = 53.903 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 2016-07-04 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 1.65 50 98 0.068 0.068 10.6 3.7 42019
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 1.65 1.75 94.9 0.378 1.9 2.6
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 1u8u 1.65 50 39926 2093 98.01 0.18804 0.18619 0.1971 0.222 0.2306 RANDOM 20.632
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 0.23 0.67 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.318 r_dihedral_angle_4_deg 17.796 r_dihedral_angle_3_deg 15.169 r_long_range_B_refined 6.346 r_long_range_B_other 6.093 r_dihedral_angle_1_deg 5.836 r_scangle_other 4.862 r_scbond_it 3.189 r_scbond_other 3.188 r_mcangle_it 2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.318 r_dihedral_angle_4_deg 17.796 r_dihedral_angle_3_deg 15.169 r_long_range_B_refined 6.346 r_long_range_B_other 6.093 r_dihedral_angle_1_deg 5.836 r_scangle_other 4.862 r_scbond_it 3.189 r_scbond_other 3.188 r_mcangle_it 2.95 r_mcangle_other 2.949 r_mcbond_it 2.009 r_mcbond_other 1.979 r_angle_refined_deg 1.768 r_angle_other_deg 0.943 r_chiral_restr 0.114 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2823 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing