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Bile Salt Hydrolase from B. longum with covalent inhibitor bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HF0 2HF0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium acetate, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG4000, 0.2 M lithium sulfate. Protein crystallized in a 1:2 protein:crystallant ratio. Protein was incubated with inhibitor prior to tray setup and was 8.55 mg/mL final concentration.
Crystal Properties Matthews coefficient Solvent content 3.39 63.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.085 α = 90 b = 100.085 β = 90 c = 165.187 γ = 120
Symmetry Space Group P 32 2 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 PILATUS3 6M 2022-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 2.3 47.89 97.78 0.3254 0.3424 0.1054 0.996 7.05 10.4 43164 60.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 83.71 0.122 10.2
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 FREE R-VALUE 2HF0 2.3 47.89 1.33 42255 2015 97.8 0.2531 0.2508 0.2516 0.2838 0.2846 72.93
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 5.9476 f_angle_d 0.5495 f_chiral_restr 0.0441 f_plane_restr 0.0033 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4728 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing