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PqsR coinducer binding domain of Pseudomonas aeruginosa with ligand 2t : 2-(4-(3-((6-chloro-1-(2-methoxyethyl)-1H-benzo[d]imidazol-2-yl)amino)-2-hydroxypropoxy)phenyl)acetonitrile
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 292.15 in 0.1 M Trisodium citrate (pH range 5.8-6.2), 0.2 M Ammonium acetate and MPD (3-8%).
Crystal Properties Matthews coefficient Solvent content 4.88 74.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.033 α = 90 b = 119.033 β = 90 c = 115.919 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 CCD ADSC QUANTUM 315r 2019-09-01 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) 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 2.75 115.92 99.9 0.988 10.5 10.2 13152
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 2.75 2.83 100 0.816 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.8 103.3 11816 629 99.85 0.22563 0.22242 0.2329 0.28479 0.2935 RANDOM 100.035
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] 3.68 1.84 3.68 -11.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.468 r_dihedral_angle_4_deg 19.063 r_dihedral_angle_3_deg 18.888 r_long_range_B_refined 12.561 r_long_range_B_other 12.557 r_mcangle_it 8.714 r_mcangle_other 8.699 r_scangle_other 8.158 r_dihedral_angle_1_deg 7.54 r_mcbond_it 5.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.468 r_dihedral_angle_4_deg 19.063 r_dihedral_angle_3_deg 18.888 r_long_range_B_refined 12.561 r_long_range_B_other 12.557 r_mcangle_it 8.714 r_mcangle_other 8.699 r_scangle_other 8.158 r_dihedral_angle_1_deg 7.54 r_mcbond_it 5.602 r_mcbond_other 5.591 r_scbond_it 5.035 r_scbond_other 5.032 r_angle_refined_deg 1.298 r_angle_other_deg 1.105 r_chiral_restr 0.049 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing