5U09

High-resolution crystal structure of the human CB1 cannabinoid receptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3V2Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.529331% PEG400, 100mM Sodium Citrate pH5.5, 100mM magnesium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.0659.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.652α = 90
b = 80.381β = 91.72
c = 81.178γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-31MSINGLE 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)R Merge I (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
12.650.0196.90.1945.65.419781
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6996.81.4110.695.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3V2Y2.650.011108461257.880.18320.18030.2382RANDOM44.12
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]
6.051.27-2.83-3.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.488
r_dihedral_angle_4_deg20.71
r_dihedral_angle_3_deg18.966
r_dihedral_angle_1_deg8.654
r_mcangle_it6.886
r_mcbond_it4.549
r_mcbond_other4.547
r_angle_refined_deg1.2
r_angle_other_deg0.643
r_chiral_restr0.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.488
r_dihedral_angle_4_deg20.71
r_dihedral_angle_3_deg18.966
r_dihedral_angle_1_deg8.654
r_mcangle_it6.886
r_mcbond_it4.549
r_mcbond_other4.547
r_angle_refined_deg1.2
r_angle_other_deg0.643
r_chiral_restr0.249
r_gen_planes_refined0.012
r_bond_refined_d0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3762
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms119

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling