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Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C1Q PDB entry 6C1Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 6.5 289 100 mM MES, pH 6.5, 100 mM ammonium sulfate, 30% PEG400, 2% P400, 1 mM succinic acid
Crystal Properties Matthews coefficient Solvent content 3.97 69.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.457 α = 90 b = 61.71 β = 90 c = 266.517 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS EIGER X 16M 2017-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.8 30 91.9 0.183 0.202 0.083 5.3 4.9 19625 68.26
Highest Resolution Shell 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 2.8 2.85 76.5 0.774 0.862 0.367 0.708 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 6C1Q 2.798 29.333 1.35 19525 973 91.18 0.252 0.2503 0.2573 0.2796 0.2899 84.9894
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.1 f_angle_d 0.594 f_chiral_restr 0.019 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3490 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 149
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction