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PqsR (MvfR) in complex with antagonist 61
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Trisodium Citrate
200 mM Ammonium acetate
4-10% MPD
Crystal Properties Matthews coefficient Solvent content 4.51 72.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.788 α = 90 b = 119.788 β = 90 c = 116.499 γ = 120
Symmetry Space Group P 65 2 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 EIGER2 X 16M 2018-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9159 Diamond I04
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 2.65 77.59 99.9 0.806 10.7 9.3 14874
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 2.65 2.78 0.676 2
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 FOURIER SYNTHESIS FREE R-VALUE 4JVC 2.65 77.47 14841 707 99.792 0.233 0.2318 0.2321 0.2606 0.2602 99.403
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] 3.643 1.822 3.643 -11.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.292 r_dihedral_angle_3_deg 16.877 r_dihedral_angle_4_deg 12.744 r_lrange_it 12.609 r_lrange_other 12.605 r_mcangle_it 9.286 r_mcangle_other 9.282 r_scangle_it 8.571 r_scangle_other 8.567 r_dihedral_angle_1_deg 7.669
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.292 r_dihedral_angle_3_deg 16.877 r_dihedral_angle_4_deg 12.744 r_lrange_it 12.609 r_lrange_other 12.605 r_mcangle_it 9.286 r_mcangle_other 9.282 r_scangle_it 8.571 r_scangle_other 8.567 r_dihedral_angle_1_deg 7.669 r_mcbond_it 5.884 r_mcbond_other 5.884 r_scbond_it 5.319 r_scbond_other 5.316 r_angle_other_deg 2.325 r_angle_refined_deg 1.32 r_symmetry_nbd_refined 0.31 r_nbd_other 0.249 r_symmetry_nbd_other 0.217 r_nbd_refined 0.208 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.115 r_symmetry_xyhbond_nbd_refined 0.101 r_symmetry_xyhbond_nbd_other 0.085 r_symmetry_nbtor_other 0.065 r_chiral_restr 0.052 r_bond_other_d 0.035 r_gen_planes_other 0.005 r_bond_refined_d 0.004 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling