Computational protocol: Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy

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Protocol publication

[…] The X-ray diffraction data of the native crystals I and II, and the selenomethionine crystal were collected at 100 K at the beamlines APS 22-BM, ALS 5.0.2 and ALS 8.2.1, respectively. All X-ray diffraction data were indexed, integrated and scaled using the HKL-2000 package. The multi-wavelength anomalous diffraction (MAD) data set was solved and an initial model was built using the AutoSol and AutoBuild modules of the PHENIX package, respectively. Because the selenomethionine crystal was not isomorphous with respect to the native crystals, the initial model from the MAD data was used for molecular replacement of the native data sets using AutoMR in PHENIX. The structures were further refined by iterative model building in Coot and refinement using the PHENIX refinement module. The qualities of the final models were assessed with MolProbity; 95.3–97.0% of all φ and ψ geometries were in the most favored region, with less than 0.3% outliers in the Ramachandran statistics. All structure figures were generated using PyMOL (Schrödinger). […]

Pipeline specifications

Software tools HKL-2000, PHENIX, Coot, MolProbity, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Homo sapiens