5MZP

Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with caffeine at 2.1A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.52930.1M MES PH 5.5, 0.2M K/NA TARTRATE, 27.5-40% PEG400, 0.5-1% (V/V) (+/-)-2-METHYL-2,4-PENTANEDIOL
Crystal Properties
Matthews coefficientSolvent content
2.5852.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.442α = 90
b = 179.87β = 90
c = 139.64γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M(DOUBLE) KB MIRROR PAIR2016-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.96862DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.189.9498.70.130.9968.24.829678
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1699.90.9770.5320.4541.44.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5IU42.138.5271.3629222147998.490.19670.19550.2199
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d19.655
f_angle_d0.953
f_chiral_restr0.072
f_bond_d0.027
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3010
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms535

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing