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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 0.2 M MgCl2, 0.1 M Tris:HCl pH 8.5, 16% (w/v) PEG 4000. Crystals formed in 1:2 ratio of protein (11.8 mg/mL) to mother liquor. 2.5 uM protein was incubated with 50 uM inhibitor for 1h at 37oC. Mixture was washed 3x with buffer in a spin concentrator and then concentrated to 11.8 mg/mL final concentration.
Crystal Properties Matthews coefficient Solvent content 2.54 51.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.072 α = 90 b = 166.801 β = 116.6 c = 103.077 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 293 PIXEL DECTRIS PILATUS3 6M 2021-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.00 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 2.35 49.1 99.6 0.1771 0.208 0.1076 0.986 5.4 3.8 116293 47.52
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 2.35 2.43 99.6 1.889 2.199 1.112 0.341 0.88 3.9
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 2.35 49.1 1.34 116139 1996 99.56 0.2103 0.2097 0.2099 0.2436 0.2492 55.03
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 15.3487 f_angle_d 0.5 f_chiral_restr 0.0424 f_plane_restr 0.0031 f_bond_d 0.0022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19151 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 248
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing