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Crystal structure of PqsR (MvfR) ligand-binding domain in complex with a pyridin agonist
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 198mM MgCl2
34.7% MPD
0.1M Tris pH 7.25
10mg/ml PqsR
+ 1.5 mM 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
0.39 mM Amaranth (CAS 915-67-3)
Cryo: + 20% 2,3- RR- Butandiol
Crystal Properties Matthews coefficient Solvent content 4.75 74.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.386 α = 90 b = 121.386 β = 90 c = 114.839 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 PILATUS3 X CdTe 2M 2019-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.47690 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 2.28 105.124 95.9 0.016 1 33.9 56.4 15066 72.55
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 2.28 2.5 86.8 0.667 0.73 1.9
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 2.28 25.62 1.36 15027 1500 64.6 0.2458 0.2438 0.2427 0.2645 0.2661 79.33
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 9.9421 f_angle_d 0.9493 f_chiral_restr 0.0607 f_plane_restr 0.01 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1610 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHASER phasing PDB_EXTRACT data extraction