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Structure of the human P2Y12 receptor in complex with an antithrombotic drug
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VW7 PDB ENTRY 3VW7 (PAR1), PDB ENTRY 1M6T (BRIL) experimental model PDB 1M6T PDB ENTRY 3VW7 (PAR1), PDB ENTRY 1M6T (BRIL)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 0.05-0.15M ammonium formate, 0.1M sodium cacodylate, pH 6.0-6.5, 25-35% PEG 400, 200M AZD1283, Lipidic Cubic Phase, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.23 61.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.65 α = 90 b = 156.43 β = 111.08 c = 47.77 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 CCD MARMOSAIC 300 mm CCD mirror 2013-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 50 94.1 0.103 14.4 3.8 19116 84.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 79.5 0.958 1.2 3.1 1608
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3VW7 (PAR1), PDB ENTRY 1M6T (BRIL) 2.62 26.44 19094 990 94.18 0.2211 0.2196 0.2464 0.2782 RANDOM 106.1
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] -14.0343 1.9204 14.1675 -0.1332
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.16 t_omega_torsion 2.16 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.16 t_omega_torsion 2.16 t_angle_deg 1.05 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2886 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 127
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing BUSTER refinement HKL-2000 data reduction HKL-2000 data scaling