3NYA

Crystal structure of the human beta2 adrenergic receptor in complex with the neutral antagonist alprenolol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1293100 mM Bis-Tris Propane pH 6.6-6.8, 120 mM Na-tartrate, 3% 1,3 butanediol, 25-30% PEG 400, Lipidic Cubic Phase (LCP) Crystallization, temperature 293-295K
Crystal Properties
Matthews coefficientSolvent content
2.3848.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.577α = 90
b = 75.73β = 90
c = 173.403γ = 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
1,23.164092.10.126.43.0297248952-3
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)
1,23.163.3588.90.4482.092.831508

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 3D4S3.1637.94849745692.190.234790.231880.28962RANDOM58.619
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]
6-1.64-4.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.511
r_dihedral_angle_3_deg15.947
r_dihedral_angle_4_deg13.891
r_dihedral_angle_1_deg4.886
r_angle_refined_deg1.045
r_scangle_it1.031
r_angle_other_deg0.837
r_mcangle_it0.66
r_scbond_it0.597
r_mcbond_it0.354
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.511
r_dihedral_angle_3_deg15.947
r_dihedral_angle_4_deg13.891
r_dihedral_angle_1_deg4.886
r_angle_refined_deg1.045
r_scangle_it1.031
r_angle_other_deg0.837
r_mcangle_it0.66
r_scbond_it0.597
r_mcbond_it0.354
r_chiral_restr0.057
r_mcbond_other0.033
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3527
Nucleic Acid Atoms
Solvent Atoms7
Heterogen Atoms74

Software

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