6TOT
Crystal structure of the Orexin-1 receptor in complex with lemborexant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6TO7 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.6 | 284 | 0.1M TRISODIUM CITRATE 50mM SODIUM CHLORIDE 50mM LITHIUM SULPHATE 15-34% PEG400 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.79 | 67.52 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 59.725 | α = 90 |
b = 145.715 | β = 112.25 |
c = 71.703 | 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 | 2015-11-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.96861 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.22 | 24.02 | 63.9 | 0.999 | 12.1 | 3.8 | 35526 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.22 | 2.4 | 6.1 | 0.442 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 6TO7 | 2.22 | 24.02 | 35526 | 1789 | 63.9 | 0.207 | 0.206 | 0.239 | RANDOM | 70.74 |
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] | |
4.2219 | -0.9543 | -1.6151 | -2.6069 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
t_other_torsion | 17.82 |
t_omega_torsion | 2.6 |
t_angle_deg | 1 |
t_bond_d | 0.01 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4826 |
Nucleic Acid Atoms | |
Solvent Atoms | 43 |
Heterogen Atoms | 357 |
Software
Software | |
---|---|
Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
STARANISO | data scaling |
PHASER | phasing |