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PqsR (MvfR) in complex with antagonist 18
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JVC 4JVC, 6Q7W experimental model PDB 6Q7W 4JVC, 6Q7W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 100 mM Sodium citrate, 200 mM Ammonium acetate and 5% MPD
Crystal Properties Matthews coefficient Solvent content 4.38 71.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.911 α = 90 b = 118.911 β = 90 c = 115.464 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 2019-05-02 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 3.2 115.46 92.4 0.061 0.997 16.6 9 7628
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 3.2 3.42 0.398 0.972
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 4JVC, 6Q7W 3.201 76.972 7592 401 90.467 0.206 0.2035 0.2046 0.2613 0.2657 134.248
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] 4.477 2.238 4.477 -14.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.781 r_dihedral_angle_3_deg 15.685 r_lrange_it 13.053 r_lrange_other 13.05 r_dihedral_angle_4_deg 11.028 r_mcangle_it 9.168 r_mcangle_other 9.16 r_scangle_it 8.719 r_scangle_other 8.715 r_dihedral_angle_1_deg 6.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.781 r_dihedral_angle_3_deg 15.685 r_lrange_it 13.053 r_lrange_other 13.05 r_dihedral_angle_4_deg 11.028 r_mcangle_it 9.168 r_mcangle_other 9.16 r_scangle_it 8.719 r_scangle_other 8.715 r_dihedral_angle_1_deg 6.651 r_mcbond_it 5.835 r_mcbond_other 5.826 r_scbond_it 5.313 r_scbond_other 5.311 r_angle_refined_deg 1.236 r_angle_other_deg 1.067 r_symmetry_nbd_refined 0.222 r_nbd_refined 0.192 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.154 r_nbd_other 0.153 r_xyhbond_nbd_refined 0.122 r_symmetry_xyhbond_nbd_refined 0.08 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.038 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing