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Sphingosine-1-phosphate receptor 3 with a natural ligand.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V2Y 3V2Y, 5XLI experimental model PDB 5XLI 3V2Y, 5XLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8 293 100 mM Tris-HCl, 36% PEG 400, 80 mM Lithium Citrate
Crystal Properties Matthews coefficient Solvent content 2.91 57.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.48 α = 90 b = 247.08 β = 97.37 c = 98.61 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 EIGER X 9M 2019-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.2 43.48 100 0.732 0.738 0.996 11.02 59.872 30984 101.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.39 100 12.686 0.663 1.28 53.468
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 3V2Y, 5XLI 3.2 43.48 1.36 30953 1520 99.9 0.2429 0.2419 0.2447 0.2629 0.27 81.6066
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11060 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing