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Crystal structure of the P2Y12 receptor in complex with the inverse agonist selatogrel.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 298 0.1 M ammonium formate, 0.1 M sodium cacdylate, pH 6.0-6.5, 25-35% PEG400
Crystal Properties Matthews coefficient Solvent content 3.15 60.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.09 α = 90 b = 155.37 β = 111.48 c = 47.31 γ = 90
Symmetry Space Group C 1 2 1
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 PILATUS3 6M 2019-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.78 78.7 98.9 0.99 18.6 50.8 16554
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.78 2.87 91.6 0.5 0.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4ntj 2.78 45.68 16390 1630 98.967 0.246 0.2418 0.2432 0.2857 0.2872 87.413
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] 4.695 0.05 -6.221 1.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_3_deg 20.355 r_dihedral_angle_4_deg 13.978 r_lrange_it 11.979 r_scangle_it 7.236 r_mcangle_it 7.187 r_dihedral_angle_1_deg 5.269 r_scbond_it 4.506 r_mcbond_it 4.342 r_angle_refined_deg 0.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_3_deg 20.355 r_dihedral_angle_4_deg 13.978 r_lrange_it 11.979 r_scangle_it 7.236 r_mcangle_it 7.187 r_dihedral_angle_1_deg 5.269 r_scbond_it 4.506 r_mcbond_it 4.342 r_angle_refined_deg 0.919 r_nbtor_refined 0.322 r_symmetry_nbd_refined 0.231 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.152 r_xyhbond_nbd_refined 0.106 r_chiral_restr 0.086 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2837 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing