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S1P3 in complex with cpd-32 and spm242
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293.15 100 mM Tris-HCl, pH 8.0, 18% PEG500DME, 50 mM NaCl, 50 mM Li2SO4, 12 mM ATP
Crystal Properties Matthews coefficient Solvent content 3.32 62.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.911 α = 90 b = 301.701 β = 90 c = 70.055 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 PIXEL DECTRIS EIGER X 16M 2021-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3 38.5 99.74 0.104 8 7.9 18928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 0.104
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 3 38.5 1.35 15727 767 99.69 0.2436 0.2424 0.2475 0.2678 0.2746
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 5.453 f_angle_d 0.725 f_chiral_restr 0.047 f_plane_restr 0.006 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3712 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PHASER phasing