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Crystal structure of human adenosine A2A receptor in complex with istradefylline.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 7 293.15 PEGMME 500, potassium citrate tribasic, HEPES
Crystal Properties Matthews coefficient Solvent content 2.47 50.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.59 α = 97.72 b = 134.84 β = 91.44 c = 42.15 γ = 89.38
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2017-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.2 49.57 99.9 0.662 0.701 0.225 0.924 3.9 9.2 26841
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) Redundancy Number Unique Reflections (All) 1 3.2 3.42 100 2.292 2.429 0.786 0.444 9.1
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 3VGA 3.2 49.57 25406 1434 99.95 0.2211 0.2181 0.2198 0.2769 0.2718 RANDOM 42.243
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] 2.1 -0.44 -0.12 -4.46 -0.41 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_3_deg 21.824 r_dihedral_angle_4_deg 20.792 r_dihedral_angle_1_deg 7.604 r_angle_refined_deg 1.564 r_angle_other_deg 1.195 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_3_deg 21.824 r_dihedral_angle_4_deg 20.792 r_dihedral_angle_1_deg 7.604 r_angle_refined_deg 1.564 r_angle_other_deg 1.195 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11097 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 222
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing