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S1P3 in complex with CYM52581 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, 20% PEG600, 60 mM Li2SO4, 15% DMSO
Crystal Properties Matthews coefficient Solvent content 3.47 64.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.57 α = 90 b = 299.58 β = 90 c = 67.46 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 2021-06-15 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 3.6 29.7 99.53 0.05 4.4 7.3 9019
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.7 0.02
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 3.6 29.66 1.34 9019 451 99.82 0.2338 0.2314 0.2336 0.281 0.2854
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 5.555 f_angle_d 1.182 f_chiral_restr 0.078 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3693 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling BUSTER refinement