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FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, borolane-based compound Q41 bound in crystal form 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8G48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291.15 16 uL 11.2 mg/mL FphE (10 mM HEPES pH 7.5, 100 mM NaCl) were mixed with 6 uL Q41 (50 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-Q41 solution was mixed with 0.3 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 180 mM Potassium Thiocyanate, 100 mM Sodium acetate pH 5.5, 22.5% PEG 2000 MME. Crystal was frozen in a solution of ~25% glycerol, 75% reservoir.
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 212.286 α = 90 b = 212.286 β = 90 c = 212.286 γ = 90
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 2.5 47.47 99.9 0.122 0.124 0.022 1 23.7 31.2 54846
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 2.5 2.57 98.4 2.179 2.215 0.394 0.692 30.5
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 2.5 47.47 1.34 54834 2769 99.85 0.185 0.1831 0.1832 0.2221 0.2222
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 16.973 f_angle_d 1.008 f_chiral_restr 0.057 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8800 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing