8ESL
Bile Salt Hydrolase from a Bacteroidales species with covalent inhibitor bound
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.1 M HEPES: NaOH, pH 7.5, 25% (w/v) PEG 1000. 50 mL protein at 2.5 uM was incubated with 50 uM inhibitor for 1h at 37oC. Mixture was washed 3x with buffer in a spin concentrator and then concentrated to 6.77 mg/mL final concentration. Crystals formed in conditions with 1:2 ratio of protein:mother liquor. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.27 | 45.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 63.142 | α = 90 |
b = 66.812 | β = 90 |
c = 321.831 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2022-02-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 23-ID-B | 1.00 | APS | 23-ID-B |
Data Collection
Overall | |||||||||||||||||||
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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 | 3.11 | 45.07 | 94.77 | 0.2399 | 0.2875 | 0.1551 | 0.978 | 3.81 | 3.4 | 24835 | 92.36 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 3.11 | 3.221 | 80.39 | 1.71 | 2.057 | 1.115 | 0.121 | 0.74 | 3.3 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | AlphaFold2 model of the protein | 3.11 | 45.07 | 1.33 | 24154 | 2001 | 94.82 | 0.2769 | 0.2769 | 0.3051 | 90.79 |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 5.715 |
f_angle_d | 0.4099 |
f_chiral_restr | 0.0403 |
f_plane_restr | 0.0043 |
f_bond_d | 0.0018 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8852 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 124 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |