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Structure of the quorum quenching lactonase GcL D122N mutant - bimetallic metal center - C2 space group
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 3.71 66.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.77 α = 90 b = 109.11 β = 116.42 c = 97.17 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 2017-03-01 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) 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 2.25 73.93 98.4 0.998 12.49 4.08 70302
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 2.25 2.35 0.925
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 2.25 73.93 66783 3515 98.65 0.20931 0.20801 0.2121 0.23369 0.2365 RANDOM 54.971
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] -0.31 0.3 0.08 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.432 r_long_range_B_other 11.164 r_long_range_B_refined 11.156 r_scangle_other 9.354 r_dihedral_angle_2_deg 6.732 r_scbond_it 6.63 r_scbond_other 6.617 r_mcangle_other 6.364 r_mcangle_it 6.363 r_dihedral_angle_1_deg 5.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.432 r_long_range_B_other 11.164 r_long_range_B_refined 11.156 r_scangle_other 9.354 r_dihedral_angle_2_deg 6.732 r_scbond_it 6.63 r_scbond_other 6.617 r_mcangle_other 6.364 r_mcangle_it 6.363 r_dihedral_angle_1_deg 5.688 r_mcbond_other 4.904 r_mcbond_it 4.903 r_angle_refined_deg 0.686 r_angle_other_deg 0.244 r_chiral_restr 0.034 r_gen_planes_refined 0.002 r_bond_refined_d 0.001 r_bond_other_d r_dihedral_angle_4_deg r_gen_planes_other 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 6747 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing