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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 10% (w/v) PEG 4000, 20% (v/v) isopropanol. Protein was incubated with probe and then concentrated to 7.08 mg/mL. Protein crystallized in a 1:2 protein:crystallant ratio.
Crystal Properties Matthews coefficient Solvent content 3.3 62.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.44 α = 90 b = 108.44 β = 90 c = 161.518 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 1.03 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 2.03 48.22 96.9 0.2126 0.2302 0.0838 0.986 6.08 6.2 62279 41.42
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 2.03 2.103 88.3 1.811 2.044 0.9079 0.146 0.6 4.2
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 7SVF 2.03 48.22 1.34 61189 1999 96.78 0.1872 0.1859 0.1857 0.2264 0.2259 43.43
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 7.4234 f_angle_d 0.8269 f_chiral_restr 0.0533 f_bond_d 0.0069 f_plane_restr 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4979 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing