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FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone-peptide 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 6.5 291.15 10 uL 15 mg/mL FphE (10 mM HEPES pH 7.5, 100 mM NaCl) were mixed with 4 uL Oxadiazolone-peptide-ligand (10 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-ligand solution was mixed with 0.3 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 180 mM Magnesium chloride, 100 mM MES pH 6.5, 22.5% PEG 2000 MME. Crystal was frozen in a solution of ~25% Ethylene glycol, 75% reservoir.
Crystal Properties Matthews coefficient Solvent content 2.07 40.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.107 α = 90 b = 74.583 β = 90.95 c = 73.555 γ = 90
Symmetry Space Group P 1 21 1
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 2024-03-02 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 1.54 47.1 99.7 0.076 0.083 0.032 0.998 11.9 6.8 75123
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 1.54 1.57 94.1 1.237 1.343 0.514 0.56 6.6
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 1.54 39.82 1.34 75083 3604 99.63 0.1568 0.1555 0.1555 0.183 0.183
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 7.019 f_angle_d 1.067 f_chiral_restr 0.062 f_plane_restr 0.011 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4386 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing