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Dimeric structure of a Quorum-Quenching metallo-hydrolase, LrsL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 1.6 M tri-Sodium citrate tribasic
Crystal Properties Matthews coefficient Solvent content 3.02 59.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.51 α = 90 b = 166.51 β = 90 c = 166.51 γ = 90
Symmetry Space Group P 41 3 2
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 2022-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.987 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.89 46.18 99.97 0.1542 0.1552 0.01717 1 31.63 81.3 63574 44.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.958 99.98 6.561 6.601 0.7185 0.368 0.71 83.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1P9E 1.89 46.18 63574 2000 99.881 0.192 0.1908 0.1908 0.2349 0.2351 47.577
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_3_deg 16.198 r_dihedral_angle_6_deg 16.01 r_lrange_it 10.418 r_scangle_it 8.044 r_dihedral_angle_1_deg 7.404 r_dihedral_angle_2_deg 7.349 r_scbond_it 5.816 r_mcangle_it 5.536 r_mcbond_it 4.208 r_angle_refined_deg 1.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.198 r_dihedral_angle_6_deg 16.01 r_lrange_it 10.418 r_scangle_it 8.044 r_dihedral_angle_1_deg 7.404 r_dihedral_angle_2_deg 7.349 r_scbond_it 5.816 r_mcangle_it 5.536 r_mcbond_it 4.208 r_angle_refined_deg 1.719 r_nbtor_refined 0.313 r_nbd_refined 0.211 r_symmetry_nbd_refined 0.198 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.137 r_chiral_restr 0.11 r_metal_ion_refined 0.048 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4386 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling BALBES phasing