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Crystal structure of the human beta2 adrenergic receptor in complex with the neutral antagonist alprenolol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D4S PDB entry 3D4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 293 100 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 coefficient Solvent content 2.38 48.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.577 α = 90 b = 75.73 β = 90 c = 173.403 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2009-11-19 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2009-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D 2 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 3.16 40 92.1 0.12 6.4 3.02 9724 8952 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 3.16 3.35 88.9 0.448 2.09 2.83 1508
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3D4S 3.16 37.94 8497 456 92.19 0.23479 0.23188 0.2317 0.28962 0.2808 RANDOM 58.619
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.511 r_dihedral_angle_3_deg 15.947 r_dihedral_angle_4_deg 13.891 r_dihedral_angle_1_deg 4.886 r_angle_refined_deg 1.045 r_scangle_it 1.031 r_angle_other_deg 0.837 r_mcangle_it 0.66 r_scbond_it 0.597 r_mcbond_it 0.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.511 r_dihedral_angle_3_deg 15.947 r_dihedral_angle_4_deg 13.891 r_dihedral_angle_1_deg 4.886 r_angle_refined_deg 1.045 r_scangle_it 1.031 r_angle_other_deg 0.837 r_mcangle_it 0.66 r_scbond_it 0.597 r_mcbond_it 0.354 r_chiral_restr 0.057 r_mcbond_other 0.033 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3527 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 74
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling