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FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, Oxadiazolone JJ004 bound
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 8.5 289.15 13 uL 19 mg/mL FphE (10 mM HEPES pH 7.5, 10 0mM NaCl) were mixed with 5 uL JJ004 (10 mM in DMSO) and incubated at 18C overnight. 0.15 uL FphE-JJ004 solution was mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 0.18 M Magnesium chloride, 0.1 M Tris pH 8.5, 22.5 % w/v Polyethylene glycol monomethyl ether 2000. Crystal was frozen in a solution of ~25% glycerol, 75% reservoir.
Crystal Properties Matthews coefficient Solvent content 2.04 39.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.743 α = 90 b = 74.271 β = 91.7 c = 73.638 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 9M 2023-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 39.99 98 0.037 0.041 0.018 1 17.5 5.3 73321
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 1.56 95.1 1.051 1.166 0.498 0.598 5.2
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 1.54 39.99 1.35 73279 3528 97.75 0.1579 0.1565 0.156 0.1846 0.184
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 9.573 f_angle_d 1.077 f_chiral_restr 0.059 f_plane_restr 0.017 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4386 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 56
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing