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Crystal structure of P2Y12 receptor in complex with 2MeSATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PXZ PDB ENTRY 4PXZ and 1M6T experimental model PDB 1M6T PDB ENTRY 4PXZ and 1M6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Lipidic cubic phase (LCP) 6 293 35-40% PEG 400, 0.15-0.20M ammonium tartrate, 4% v/v MPD, 0.1M sodium citrate, pH 6.0, Lipidic cubic phase (LCP), temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.65 α = 90 b = 65.11 β = 95.5 c = 100.74 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 225 mm CCD mirrors 2013-12-08 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) 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 3.1 30 92.2 0.222 5.6 3.2 8273 87.79
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 3.1 3.27 91.2 0.922 2.2 2.9
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 PDB ENTRY 4PXZ and 1M6T 3.1 28.81 8273 422 92.33 0.2239 0.2216 0.2392 0.2652 0.2882 RANDOM 88.61
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] 2.8922 0.6083 -0.3371 -2.5552
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.24 t_omega_torsion 1.68 t_angle_deg 0.87 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.24 t_omega_torsion 1.68 t_angle_deg 0.87 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 3046 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 65
Software Software Software Name Purpose PHASER phasing BUSTER refinement XDS data reduction XDS data scaling