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FphD, Staphylococcus epidermidis fluorophosphonate-binding serine hydrolases D, apo form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FLE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289.15 0.3uL 7.1 mg/ml FphD S. epidermidis (10mM HEPES pH 7.5, 100mM NaCl) were mixed with 0.15uL of reservoir solution. Sitting drop reservoir contained 30ul of 0.1 M potassium thiocyanate, 1.0 M sodium acetate pH 5.5. Crystal appeared after 3 days at 16C and grew larger for another 1 week when it was frozen in a solution of ~25% glycerol, 75% reservoir.
Crystal Properties Matthews coefficient Solvent content 1.86 33.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.619 α = 90 b = 129.713 β = 111.28 c = 45.161 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 2025-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95373 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 1.7 43.24 98.7 0.116 0.126 0.048 0.998 10.4 6.7 44977
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 1.7 1.73 95.5 0.961 1.05 0.414 0.32 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 1.7 42.08 1.34 44934 2348 98.58 0.1784 0.1769 0.1764 0.2059 0.2055
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 16.526 f_angle_d 0.788 f_chiral_restr 0.056 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3930 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction