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FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, borolane-based compound Q41 bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8T87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289.15 13uL 19.0 mg/mL FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 5uL Q41 (50mM in DMSO) and incubated at 18C overnight. 0.3 uL FphE-Q41 solution was mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 180mM Calcium acetate, 100mM Tris pH 8.5, 22.5% PEG 2000 MME. Crystal was frozen in a solution of ~25% Ethylene glycol, 75% reservoir.
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.887 α = 90 b = 77.993 β = 90 c = 110.457 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2023-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.97 45.8 99.9 0.084 0.09 0.032 0.999 13.9 8 41115
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.02 98.5 1.093 1.166 0.401 0.704 8.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.97 45.8 1.34 41047 2064 99.86 0.1695 0.1675 0.167 0.2037 0.2029
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 7.215 f_angle_d 1.195 f_chiral_restr 0.063 f_plane_restr 0.017 f_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4386 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing