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Structure of the quorum quenching lactonase GcL I237M mutant
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 1.0 - 1.25 M ammonium sulfate and 0.1 M sodium acetate pH 4.0 - 5.5
Crystal Properties Matthews coefficient Solvent content 2.81 56.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.4 α = 90 b = 110.3 β = 115.9 c = 79.4 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 EIGER X 16M 2020-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.99184 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.3 64.23 94.9 0.998 19.44 3.74 48202
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 0.975
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.35 64.17 43062 2267 95.24 0.1851 0.18437 0.1915 0.19915 0.2027 RANDOM 33.759
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 -2.83 5.34 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.291 r_long_range_B_refined 6.791 r_long_range_B_other 6.783 r_dihedral_angle_1_deg 5.785 r_scangle_other 5.176 r_mcangle_it 4.006 r_mcangle_other 4.006 r_scbond_it 3.424 r_scbond_other 3.419 r_mcbond_it 2.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.291 r_long_range_B_refined 6.791 r_long_range_B_other 6.783 r_dihedral_angle_1_deg 5.785 r_scangle_other 5.176 r_mcangle_it 4.006 r_mcangle_other 4.006 r_scbond_it 3.424 r_scbond_other 3.419 r_mcbond_it 2.766 r_mcbond_other 2.762 r_dihedral_angle_2_deg 1.1 r_angle_refined_deg 0.923 r_angle_other_deg 0.379 r_chiral_restr 0.044 r_bond_refined_d 0.004 r_gen_planes_refined 0.002 r_gen_planes_other 0.001 r_bond_other_d r_dihedral_angle_4_deg 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 6706 Nucleic Acid Atoms Solvent Atoms 669 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing