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Bile Salt Hydrolase B from Lactobacillus gasseri with covalent inhibitor bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SVH 7SVH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH, pH 10.5, 2M Ammonium Sulfate. Crystals formed in a 2:1 ratio of protein: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 8 mg/mL final concentration.
Crystal Properties Matthews coefficient Solvent content 3.39 63.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.362 α = 90 b = 157.362 β = 90 c = 140.718 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 PILATUS3 6M 2021-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03 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 2.18 48.95 99.8 0.125 0.128 0.028 1 16.7 20.8 100941 63.96
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 2.18 2.258 98.6 6.367 6.518 1.38 0.209 0.57 21.7
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 7SVH 2.18 48.95 1.33 100941 3753 99.22 0.2366 0.2359 0.2358 0.2551 0.2549 69.93
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 6.4014 f_angle_d 0.4664 f_chiral_restr 0.0426 f_plane_restr 0.0029 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4916 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing