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PqsR (MvfR) in complex with antagonist 12
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 6% MPD
Crystal Properties Matthews coefficient Solvent content 4.38 71.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.79 α = 90 b = 120.79 β = 90 c = 114.393 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 2.95 60.47 100 0.089 0.998 12.6 9.6 10879
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 2.95 3.13 1.079 0.917
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 2.95 60.47 10857 528 99.899 0.202 0.1995 0.1997 0.2565 0.2591 120.825
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] 4.006 2.003 4.006 -12.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.883 r_lrange_it 24.169 r_lrange_other 24.168 r_scangle_it 19.096 r_scangle_other 19.088 r_mcangle_it 17.916 r_mcangle_other 17.913 r_dihedral_angle_3_deg 17.727 r_dihedral_angle_4_deg 16.669 r_scbond_it 13.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.883 r_lrange_it 24.169 r_lrange_other 24.168 r_scangle_it 19.096 r_scangle_other 19.088 r_mcangle_it 17.916 r_mcangle_other 17.913 r_dihedral_angle_3_deg 17.727 r_dihedral_angle_4_deg 16.669 r_scbond_it 13.413 r_scbond_other 13.407 r_mcbond_it 13.174 r_mcbond_other 13.163 r_dihedral_angle_1_deg 7.503 r_angle_refined_deg 1.671 r_angle_other_deg 1.262 r_symmetry_nbd_refined 0.431 r_nbd_other 0.415 r_symmetry_xyhbond_nbd_refined 0.232 r_nbd_refined 0.228 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_other 0.169 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.07 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 5 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing