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FphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289.15 0.2 uL ~8.5 mg/ml FphF (20 mM HEPES pH 7.5, 10 mM NaCl) were mixed with 0.1 uL FphF crystal seeds (in 54.4% Tacsimate pH 7.0, 0.1 M Bis-Tris propane pH 6.5, 8% Polypropylene glycol P 400) and 0.2 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 2.8 M Sodium acetate. Crystals were soaked for ~20 seconds in 75% reservoir solution and 25% ethylenglycol prior to freezing in liquid nitrogen
Crystal Properties Matthews coefficient Solvent content 2.13 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.145 α = 90 b = 87.145 β = 90 c = 453.6 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 16M 2019-07-31 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 1.71 49.16 99.9 0.128 0.13 0.025 0.999 16.5 27.3 112281
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 1.71 1.74 97.8 3.155 3.215 0.605 0.581 27.2
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 4rgy 1.71 43.57 1.92 112050 10223 99.86 0.1777 0.1765 0.1832 0.2008 0.2073 39.4965
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 8236 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction