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Crystal structure of acyl-CoA thioesterase tesB from Yersinia pestis in complex with coenzyme A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QFW pdb entry 4QFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 296 22% PEG 3350, 200 mM sodium malonate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.31 46.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.976 α = 90 b = 171.369 β = 109.51 c = 73.656 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 ADSC QUANTUM 210r 2014-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 45.91 100 0.105 10.3 7.7 60243
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 2.2 2.26 100 0.491 4.1 7.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 4QFW 2.2 85.68 60167 57177 2995 99.93 0.20454 0.20137 0.2043 0.26592 0.2668 RANDOM 37.179
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] 0.02 0.02 -0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.68 r_dihedral_angle_4_deg 15.753 r_dihedral_angle_3_deg 14.84 r_dihedral_angle_1_deg 6.653 r_mcangle_it 4.137 r_scbond_it 3.219 r_mcbond_it 2.814 r_mcbond_other 2.814 r_angle_refined_deg 1.487 r_angle_other_deg 0.791
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.68 r_dihedral_angle_4_deg 15.753 r_dihedral_angle_3_deg 14.84 r_dihedral_angle_1_deg 6.653 r_mcangle_it 4.137 r_scbond_it 3.219 r_mcbond_it 2.814 r_mcbond_other 2.814 r_angle_refined_deg 1.487 r_angle_other_deg 0.791 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8607 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement PHASER phasing PHENIX refinement XDS data reduction Aimless data scaling Blu-Ice data collection