4S0V

Crystal structure of the human OX2 orexin receptor bound to the insomnia drug Suvorexant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DKLPDB entries 4DKL and 2BFW
experimental modelPDB 2BFWPDB entries 4DKL and 2BFW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Lipidic Cubic Phase (LCP)5.929331% PEG 400, 0.1 M sodium citrate, 0.2 M sodium formate, 3%(w/v) hexanediol, pH 5.9, Lipidic Cubic Phase (LCP), temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.550.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.358α = 90
b = 75.819β = 111.71
c = 96.335γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.5501002230522305-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5499

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entries 4DKL and 2BFW2.543.7171.35197671877295584.190.19720.19720.242RANDOM
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_d12.36
f_angle_d0.745
f_chiral_restr0.025
f_bond_d0.004
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3810
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms40

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling