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Crystal structure of PqsR (MvfR) ligand-binding domain in complex with 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
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 20% MPD, 30mM magnesium formate,120 mM Lithium citrate, 100mM MES pH 5.6,
10mg/ml PqsR + 1mM 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
Cryo: + 20% MPD
Crystal Properties Matthews coefficient Solvent content 5.26 76.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.319 α = 90 b = 120.319 β = 90 c = 115.201 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 PILATUS 2M 2019-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 2.74 104.199 95.2 0.09 1 32.6 36.2 9271 90.27
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 2.74 2.985 3.587 0.61
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 2.74 60.16 1.37 9267 463 69.13 0.2476 0.2461 0.2454 0.2749 0.2699 92.45
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 7.2364 f_angle_d 0.8063 f_chiral_restr 0.0557 f_plane_restr 0.0105 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1553 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 29
Software Software Software Name Purpose PHENIX refinement AutoProcess data reduction STARANISO data scaling PHASER phasing PDB_EXTRACT data extraction