9H37 | pdb_00009h37

Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with compound 9, a novel nanomolar A2A receptor antagonist from modern hit-finding with structure-guided de novo design


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5IU4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2930.1 M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol and 0.5 mM theophylline
Crystal Properties
Matthews coefficientSolvent content
2.5752.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.46α = 90
b = 178.853β = 90
c = 139.696γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE CdTe 9M2024-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.6199DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.71544.71390.70.32780.33350.06040.98713.9730.147571
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.7151.77629.97.33647.45331.30730.481.3932.121319

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.71525.1147547231188.70.20210.20120.19490.22030.2174RANDOM32.74
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]
0.70113.443-4.1441
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.33
t_omega_torsion2.99
t_angle_deg0.82
t_bond_d0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2977
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms379

Software

Software
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
autoPROCdata processing
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing