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Crystal structure of PqsR (MvfR) ligand-binding domain in complex with compound N-((2-(4-phenoxyphenyl)thiazol-5-yl)methyl)-2-(trifluoromethyl)pyridin-4-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.7 M Sodium chloride
15 %(v/v) Glycerol
85 mM Sodium acetate pH 4.6
Protein: 7.5 mg/ml
Compound: 1.5 mM
Crystal Properties Matthews coefficient Solvent content 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.018 α = 90 b = 122.61 β = 90 c = 112.784 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 6M-F 2017-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.9780 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.67 112.8 94 0.032 0.999 14.8 13.3 14428 65.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.67 2.67 0.427 0.732 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2Q7V 2.67 53.86 1.35 14418 692 63.77 0.2102 0.2084 0.2084 0.2451 0.2436 65.49
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.3121 f_angle_d 1.458 f_chiral_restr 0.0658 f_plane_restr 0.0189 f_bond_d 0.0124
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3169 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction STARANISO data scaling PHENIX phasing