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Bile Salt Hydrolase A from Lactobacillus gasseri with chenodeoxycholate and taurine bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 18% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3 streak seeded with crystals grown in 20% (w/v) PEG 3350, 0.2M Ammonium chloride pH 6.3. Crystals were grown in a protein (9.55 mg/mL):mother liquor ratio of 1:2. Crystal seeds were streaked into this condition from a broad screen hit and then the resultant crystals were soaked in 1:1 ratio of mother liquor:100 mM TCDCA for 24h before looping.
Crystal Properties Matthews coefficient Solvent content 2.88 57.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.147 α = 90 b = 153.115 β = 105.795 c = 94.979 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 100 PIXEL DECTRIS PILATUS3 6M 2020-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 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 1.35 29.34 92.9 0.09959 0.1158 0.05829 0.995 6.16 3.8 332715 20.08
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 1.352 1.4 72.4 1.518 1.814 0.9715 0.317 0.44 3.4
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 2HEZ 1.35 29.34 1.33 327788 1965 92.9 0.1778 0.1777 0.1773 0.2 0.1984 25.19
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 8.3802 f_angle_d 0.8578 f_chiral_restr 0.083 f_bond_d 0.0062 f_plane_restr 0.0056
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9783 Nucleic Acid Atoms Solvent Atoms 1386 Heterogen Atoms 112
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing