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FphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, substrate bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VH9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289.15 0.4 uL ~8.0 mg/mL FphF (10 mM HEPES pH 7.5, 10 mM NaCl) were mixed with 0.07 uL ligand solution (~0.5 mM 4-Methylumbelliferyl heptanoate in 100% DMSO) and 0.4 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 0.8 M Sodium formate, 0.1 M Tris pH 7.5, 10 % w/v PEG 8000 and 10 % w/v PEG 1000. Crystals were soaked for ~15 seconds in 75% reservoir solution and 25% glycerol prior to freezing in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.12 42.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.957 α = 90 b = 86.957 β = 90 c = 454.712 γ = 120
Symmetry Space Group P 61 2 2
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 2020-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.954 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 2.89 49.19 99.4 0.223 0.235 0.069 0.988 7.7 9.1 23922
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 2.89 3.07 97.4 1.137 1.213 0.38 0.524 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 6VH9 2.89 49.19 1.92 23797 2067 97.19 0.2271 0.2253 0.2342 0.2606 0.2704 43.9473
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8152 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 32
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction