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Crystal structure of P2Y12 receptor in complex with 2MeSADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VW7 PDB ENTRY 3VW7 and 1M6T experimental model PDB 1M6T PDB ENTRY 3VW7 and 1M6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Lipidic cubic phase (LCP) 5 293 30-40% PEG 400, 0.30-0.45M ammonium acetate, citrate, 3% v/v 1-Propanol, 0.1 M sodium citrate, pH 5.0, Lipidic cubic phase (LCP), temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.11 α = 90 b = 104.17 β = 90 c = 169.43 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 CCD MARMOSAIC 225 mm CCD mirrors 2013-12-08 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD mirrors 2013-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU 2 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 2.5 50 100 0.194 12.4 16.5 20345 60.18
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 2.5 2.63 100 0.995 2.3 8.1
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 3VW7 and 1M6T 2.5 28.88 20345 1041 100 0.202 0.2005 0.2079 0.2297 0.2404 RANDOM 63.74
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] 5.5747 -14.2671 8.6924
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.39 t_omega_torsion 2.56 t_angle_deg 1.03 t_bond_d 0.01 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 3.39 t_omega_torsion 2.56 t_angle_deg 1.03 t_bond_d 0.01 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 3133 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 113
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing BUSTER refinement XDS data reduction XDS data scaling