Computational protocol: Imperfect interface of Beclin1 coiled-coil domain regulates homodimer and heterodimer formation with Atg14L and UVRAG

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Protocol publication

[…] Crystals were grown at 16 °C by the hanging drop vapour diffusion method mixing 1 μl of Beclin 1 CC domain at 50∼52 mg ml−1 with 1 μl of reservoir solution containing 45% 2-methyl-2,4-pentadiol, 2% PEG400, and 100 mM Tris buffer (pH 8.2). The Au derivative was obtained by soaking crystals in reservoir solution containing 2 mM AuCl4 for 2 h. The iodine derivative was obtained by growing crystals in reservoir solution with 300 mM NH4I added. All data were collected at 100 K on our in-house X-ray system (MicroMax 007 HF, Rigaku), indexed and integrated by MOSFLM, and scaled by the SCALA module in the CCP4 suite (http://www.ccp4.ac.uk/). The Au and iodine sites were located and refined using SOLVE and further refined using MLPHARE and DM modules in CCP4 to build an interpretable electron density map. The structure was built manually using COOT and the final structure was refined using REFMAC module in CCP4. Statistics were summarized in . The coordinates of Beclin 1 CC domain has been deposited to Protein Data Bank (PDB ID 3Q8T). The structure figures were prepared using the CCP4 mg package in CCP4. […]

Pipeline specifications

Software tools iMosflm, CCP4, Coot
Applications Small-angle scattering, Protein structure analysis
Chemicals Phosphatidylinositols