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PqsR (MvfR) in complex with antagonist 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Q7W 6q7w, 4jvc experimental model PDB 4JVC 6q7w, 4jvc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 100 mM Sodium citrate, 200 mM Ammonium acetate, 5% MPD
Crystal Properties Matthews coefficient Solvent content 4.38 71.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.266 α = 90 b = 120.266 β = 90 c = 115.038 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 EIGER X 16M 2019-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.15 60.13 95.7 0.084 0.97 13.9 10.1 8476
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.37 0.803 0.966
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 6q7w, 4jvc 3.15 60.13 8476 406 94.524 0.198 0.1953 0.1966 0.2411 0.2384 131.882
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] 4.972 2.486 4.972 -16.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.295 r_lrange_it 22.707 r_lrange_other 22.705 r_scangle_it 18.016 r_scangle_other 18.008 r_dihedral_angle_3_deg 17.259 r_dihedral_angle_4_deg 16.568 r_mcangle_it 16.014 r_mcangle_other 16.009 r_scbond_it 12.879
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.295 r_lrange_it 22.707 r_lrange_other 22.705 r_scangle_it 18.016 r_scangle_other 18.008 r_dihedral_angle_3_deg 17.259 r_dihedral_angle_4_deg 16.568 r_mcangle_it 16.014 r_mcangle_other 16.009 r_scbond_it 12.879 r_scbond_other 12.873 r_mcbond_other 11.973 r_mcbond_it 11.968 r_dihedral_angle_1_deg 8.288 r_angle_refined_deg 1.653 r_angle_other_deg 1.294 r_symmetry_nbd_refined 0.328 r_symmetry_xyhbond_nbd_refined 0.306 r_nbd_other 0.246 r_nbd_refined 0.225 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.134 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing