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Structure of the Quorum Quenching lactonase from Parageobacillus caldoxylosilyticus - free
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R2D
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. Diffraction quality crystals appeared after 1 d at 292 K
Crystal Properties Matthews coefficient Solvent content 2.88 57.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.42 α = 90 b = 108.68 β = 115.84 c = 78.74 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 2018-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03323 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.6 63.93 99.6 0.033 0.1 26.5 4.17 602221
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 99.7 0.645 0.994 3.1 4.15
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 2r2d 1.6 63.93 137203 7222 99.76 0.14178 0.1394 0.1524 0.1873 0.1958 RANDOM 33.224
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] 0.22 -0.26 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.844 r_sphericity_free 27.542 r_sphericity_bonded 21.389 r_dihedral_angle_4_deg 16.892 r_dihedral_angle_3_deg 13.893 r_rigid_bond_restr 7.741 r_scangle_other 7.572 r_scbond_it 6.921 r_scbond_other 6.92 r_long_range_B_refined 6.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.844 r_sphericity_free 27.542 r_sphericity_bonded 21.389 r_dihedral_angle_4_deg 16.892 r_dihedral_angle_3_deg 13.893 r_rigid_bond_restr 7.741 r_scangle_other 7.572 r_scbond_it 6.921 r_scbond_other 6.92 r_long_range_B_refined 6.848 r_long_range_B_other 6.848 r_dihedral_angle_1_deg 5.759 r_mcangle_it 5.173 r_mcangle_other 5.173 r_mcbond_it 4.694 r_mcbond_other 4.657 r_angle_other_deg 0.898 r_angle_refined_deg 0.696 r_chiral_restr 0.037 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6711 Nucleic Acid Atoms Solvent Atoms 657 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing