7SVG

Bile Salt Hydrolase A from Lactobacillus gasseri with chenodeoxycholate and taurine bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HEZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29318% (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 coefficientSolvent content
2.8857.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.147α = 90
b = 153.115β = 105.795
c = 94.979γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0APS23-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3529.3492.90.099590.11580.058290.9956.163.833271520.08
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)RedundancyNumber Unique Reflections (All)
11.3521.472.41.5181.8140.97150.3170.443.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2HEZ1.3529.341.33327788196592.90.17780.17770.225.19
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d8.3802
f_angle_d0.8578
f_chiral_restr0.083
f_bond_d0.0062
f_plane_restr0.0056
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9783
Nucleic Acid Atoms
Solvent Atoms1386
Heterogen Atoms112

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing