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Crystal structure of human adenosine A2A receptor (construct A2A-PSB2-bRIL) complexed with the partial antagonist LUF5834 at the orthosteric pocket
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IU4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.2 293 23% (w/v) PEG400, 90 mM sodium thiocyanate, 100 mM sodium citrate pH 5.2, and 2% (w/v) 2,5 hexandiol
Crystal Properties Matthews coefficient Solvent content 2.59 52.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.556 α = 90 b = 179.693 β = 90 c = 140.454 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS PILATUS 6M 2022-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97621 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.43 89.85 86.4 0.264 0.076 0.997 7.9 12.1 16837 43.05
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.59 25 2.201 0.609 0.493 1.3 12.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 2.43 70.23 1.34 16825 866 86.35 0.2069 0.2029 0.2069 0.2813 0.275
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 Key Refinement Restraint Deviation f_dihedral_angle_d 15.519 f_angle_d 1.422 f_chiral_restr 0.055 f_bond_d 0.013 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3019 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 251
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling STARANISO data scaling autoPROC data processing