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Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bound to substrate 3-oxo-C12-AHL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6N9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 Concentrated protein samples 10mg.mL-1, ammonium sulfate 1 to 2.25M, 0.1M sodium acetate. Soaking in 20 mM of C12 AHL for 5 min. Diffraction quality crystals appeared after 1 d at 292 K
Crystal Properties Matthews coefficient Solvent content 2.86 57.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.01 α = 90 b = 108.59 β = 115.75 c = 78.6 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 PIXEL DECTRIS PILATUS 6M 2018-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03333 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) CC (Half) 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 1.75 70.8 99.2 0.051 0.059 0.999 15.21 3.98 109519
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.85 99.5 0.419 0.48 0.947 3.32 4.07
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 6N9I 1.75 70.8 104043 5476 99.33 0.17894 0.17597 0.1859 0.23481 0.241 RANDOM 23.912
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] 0.1 -0.05 -0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.538 r_sphericity_free 26.558 r_sphericity_bonded 15.976 r_dihedral_angle_4_deg 14.388 r_dihedral_angle_3_deg 13.905 r_rigid_bond_restr 10.352 r_scangle_other 5.836 r_dihedral_angle_1_deg 5.65 r_long_range_B_refined 5.257 r_long_range_B_other 5.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.538 r_sphericity_free 26.558 r_sphericity_bonded 15.976 r_dihedral_angle_4_deg 14.388 r_dihedral_angle_3_deg 13.905 r_rigid_bond_restr 10.352 r_scangle_other 5.836 r_dihedral_angle_1_deg 5.65 r_long_range_B_refined 5.257 r_long_range_B_other 5.253 r_scbond_it 5.044 r_scbond_other 5.042 r_mcangle_other 3.888 r_mcangle_it 3.886 r_mcbond_it 3.376 r_mcbond_other 3.32 r_angle_other_deg 0.987 r_angle_refined_deg 0.595 r_chiral_restr 0.03 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.002 r_bond_other_d 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 6711 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 250
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing