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) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5IU4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 293 | 0.1 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 | |
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Matthews coefficient | Solvent content |
2.57 | 52.1 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.46 | α = 90 |
b = 178.853 | β = 90 |
c = 139.696 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 XE CdTe 9M | 2024-01-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.6199 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.715 | 44.713 | 90.7 | 0.3278 | 0.3335 | 0.0604 | 0.987 | 13.97 | 30.1 | 47571 |
Highest Resolution Shell | |||||||||||||||||||
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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) | ||||||||
1.715 | 1.776 | 29.9 | 7.3364 | 7.4533 | 1.3073 | 0.48 | 1.39 | 32.12 | 1319 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.715 | 25.11 | 47547 | 2311 | 88.7 | 0.2021 | 0.2012 | 0.1949 | 0.2203 | 0.2174 | RANDOM | 32.74 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.7011 | 3.443 | -4.1441 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 15.33 |
t_omega_torsion | 2.99 |
t_angle_deg | 0.82 |
t_bond_d | 0.008 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2977 |
Nucleic Acid Atoms | |
Solvent Atoms | 129 |
Heterogen Atoms | 379 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
autoPROC | data processing |
autoPROC | data processing |
autoPROC | data reduction |
Aimless | data scaling |
PHASER | phasing |