3NY9

Crystal structure of the human beta2 adrenergic receptor in complex with a novel inverse agonist


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D4SPDB entry 3D4S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1293100 mM Tris/HCl pH 7.5-8, 5% 1,4 butanediol, 220 mM Na-formate, 27% PEG 400, Lipidic Cubic Phase (LCP) Crystallization, temperature 293-295K
Crystal Properties
Matthews coefficientSolvent content
2.448.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.58α = 90
b = 75.9β = 90
c = 174.18γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-11-19MSINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 300 mm CCD2009-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D
2SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1,22.844091.40.1317.083.841338812234-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,22.842.98820.431.992.931749

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 REPLACEMENTTHROUGHOUTPDB entry 3D4S2.8437.77116206121000.221830.218890.27839RANDOM58.384
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]
5.7-0.74-4.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.843
r_dihedral_angle_4_deg20.653
r_dihedral_angle_3_deg16.677
r_dihedral_angle_1_deg4.878
r_angle_refined_deg1.23
r_chiral_restr0.083
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3466
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms105

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling