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Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus bind to substrate C4-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 3-oxo-C12 AHL for 5 min. Diffraction quality crystals appeared after 1 d at 292 K.
Crystal Properties Matthews coefficient Solvent content 3.84 67.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.02 α = 90 b = 108.02 β = 90 c = 222.14 γ = 120
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 EIGER X 16M 2018-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033200 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.35 19.74 98.9 12.41 7.35 39818
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.45
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 2.35 19.74 37826 1991 98.89 0.16846 0.16623 0.1724 0.21093 0.2145 RANDOM 44.767
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.317 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 14.069 r_long_range_B_other 9.851 r_long_range_B_refined 9.848 r_scangle_other 7.768 r_dihedral_angle_1_deg 5.568 r_scbond_it 5.503 r_scbond_other 5.491 r_mcangle_other 4.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.317 r_dihedral_angle_4_deg 17.295 r_dihedral_angle_3_deg 14.069 r_long_range_B_other 9.851 r_long_range_B_refined 9.848 r_scangle_other 7.768 r_dihedral_angle_1_deg 5.568 r_scbond_it 5.503 r_scbond_other 5.491 r_mcangle_other 4.708 r_mcangle_it 4.705 r_mcbond_it 3.607 r_mcbond_other 3.601 r_angle_other_deg 0.749 r_angle_refined_deg 0.567 r_chiral_restr 0.028 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4492 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 229
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing