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PqsR (MvfR) in complex with antagonist 40
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 4.53 72.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.433 α = 90 b = 120.433 β = 90 c = 115.784 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 3 104.3 99.1 1 17.3 18.6 10259
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 3 3.18 0.887 1.2
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 3 77.614 10253 435 98.482 0.224 0.2218 0.2219 0.267 0.2678 111.241
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] 4.239 2.119 4.239 -13.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.148 r_dihedral_angle_3_deg 15.556 r_dihedral_angle_4_deg 15.45 r_lrange_it 13.939 r_lrange_other 13.936 r_mcangle_other 9.68 r_mcangle_it 9.676 r_scangle_it 8.834 r_scangle_other 8.831 r_dihedral_angle_1_deg 7.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.148 r_dihedral_angle_3_deg 15.556 r_dihedral_angle_4_deg 15.45 r_lrange_it 13.939 r_lrange_other 13.936 r_mcangle_other 9.68 r_mcangle_it 9.676 r_scangle_it 8.834 r_scangle_other 8.831 r_dihedral_angle_1_deg 7.003 r_mcbond_it 6.03 r_mcbond_other 6.026 r_scbond_it 5.417 r_scbond_other 5.414 r_angle_other_deg 2.318 r_angle_refined_deg 1.302 r_nbd_other 0.347 r_symmetry_nbd_refined 0.26 r_symmetry_nbd_other 0.22 r_nbd_refined 0.2 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.132 r_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.065 r_chiral_restr 0.047 r_bond_other_d 0.035 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_refined_d 0.003 r_symmetry_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling