5G53

Structure of the adenosine A2A receptor bound to an engineered G protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YDVPDB ENTRIES 2YDV, 3SN6
experimental modelPDB 3SN6PDB ENTRIES 2YDV, 3SN6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.1 M NAOAC PH 5.5, 10% PEG 2000 (IN THE PRESENCE OF CHS); OR 0.1 M NAOAC PH 5.7, 9.5% PEG 2000 MME (IN THE ABSENCE OF CHS)
Crystal Properties
Matthews coefficientSolvent content
2.958

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.632α = 90
b = 111.814β = 90
c = 161.304γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MKB MIRRORS2015-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
13.440.390.60.173.62.620898
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.43.4978.50.751.22.4

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 ENTRIES 2YDV, 3SN63.491.8919788108989.940.285370.28370.31542RANDOM76.297
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]
-1.78-3.885.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.502
r_dihedral_angle_3_deg16.014
r_dihedral_angle_4_deg13.261
r_dihedral_angle_1_deg5.295
r_mcangle_it5.207
r_scangle_it3.942
r_mcbond_other3.021
r_mcbond_it3.02
r_scbond_it2.219
r_angle_refined_deg1.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.502
r_dihedral_angle_3_deg16.014
r_dihedral_angle_4_deg13.261
r_dihedral_angle_1_deg5.295
r_mcangle_it5.207
r_scangle_it3.942
r_mcbond_other3.021
r_mcbond_it3.02
r_scbond_it2.219
r_angle_refined_deg1.149
r_angle_other_deg0.923
r_chiral_restr0.115
r_bond_refined_d0.008
r_gen_planes_refined0.004
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7247
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing