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FphE, Staphylococcus aureus fluorophosphonate-binding serine hydrolases E, boronic acid-based compound Z27 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 6.5 289.15 20uL 25.0 mg/mL FphE (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 3uL Z27 (50mM in DMSO) and incubated at 4C overnight. 0.3 uL FphE-Z27 solution was mixed with 0.15 uL of reservoir solution. Sitting drop reservoir contained 25 uL of 180mM Calcium acetate, 100mM MES pH 6.5, 22.5% PEG 2000 MME. Crystal appeared within 2.5 days at 16C and grew until 14.5 days when it was frozen in a solution of ~25% glycerol, 75% reservoir.
Crystal Properties Matthews coefficient Solvent content 2.02 39.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.723 α = 90 b = 73.971 β = 91.43 c = 73.183 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 2022-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 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 1.65 46.71 99.1 0.112 0.123 0.05 0.996 9.4 5.9 59687
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 1.65 1.68 84.3 0.944 1.072 0.494 0.536 4.4
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 1.65 39.82 1.34 59652 3011 99.04 0.1516 0.1496 0.1495 0.1893 0.1892
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 6.426 f_angle_d 1.128 f_chiral_restr 0.059 f_plane_restr 0.012 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4386 Nucleic Acid Atoms Solvent Atoms 483 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing