7TRB
CRYSTAL STRUCTURE OF FARNESOID X-ACTIVATED RECEPTOR COMPLEXED WITH COMPOUND-32 AKA (1S,3S)-N-({4-[5-(2-FLUOROPR OPAN-2-YL)-1,2,4-OXADIAZOL-3-YL]BICYCLO[2.2.2]OCTAN-1-YL}M ETHYL)-3-HYDROXY-N-[4'-(2-HYDROXYPROPAN-2-YL)-[1,1'-BIPHEN YL]-3-YL]-3-(TRIFLUOROMETHYL)CYCLOBUTANE-1-CARBOXAMIDE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3RUT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 28.5% PEG2000MME 0.1M NaAc trihydrate 0.1M MES pH 6.5 10mM BME |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.85 | 33.49 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 104.71 | α = 90 |
b = 119.26 | β = 90 |
c = 36.71 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 PILATUS 6M | 2018-11-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0 | APS | 17-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.15 | 78.69 | 92.1 | 0.09 | 10.1 | 5.8 | 17574 | 56.18 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.19 | 2.37 | 50.2 | 1.037 | 1.5 | 4.2 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3RUT | 2.15 | 26.97 | 17570 | 854 | 68.4 | 0.216 | 0.214 | 0.256 | RANDOM | 66.4 |
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] | |
-1.7637 | 0.5834 | 1.1803 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 20.27 |
t_omega_torsion | 2.29 |
t_angle_deg | 1.08 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_trig_c_planes | |
t_gen_planes | |
t_it | |
t_nbd | |
t_improper_torsion |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3607 |
Nucleic Acid Atoms | |
Solvent Atoms | 13 |
Heterogen Atoms | 92 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
autoPROC | data scaling |
PHASER | phasing |