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Bile salt hydrolase A from Lactobacillus gasseri bound to covalent probe
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SVF 7SVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium phosphate dibasic:citric acid, pH 4.2, 40% (v/v) PEG 300. Probe was incubated with protein before tray setup at 6.94 mg/mL protein concentration. Crystals formed in a 1:1 protein:crystallant ratio.
Crystal Properties Matthews coefficient Solvent content 3.29 62.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.538 α = 90 b = 108.538 β = 90 c = 160.341 γ = 90
Symmetry Space Group P 43 21 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 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 1.83 48.54 99.9 0.1765 0.1831 0.04826 0.998 12.09 14.5 84823 34.38
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 1.83 1.895 99.9 4.355 4.51 1.166 0.357 0.86 14.9
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 7SVF 1.83 48.54 1.34 84814 1999 99.99 0.2004 0.1998 0.1998 0.2247 0.2238 36.55
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 13.8657 f_angle_d 0.8983 f_chiral_restr 0.059 f_bond_d 0.0075 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4911 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 78
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing