Computational protocol: Structural basis of AMPK regulation by adenine nucleotides and glycogen

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Protocol publication

[…] All diffraction data sets were collected at 100 K using an X-ray beam with Rayomics 300 CCD detectors at the ID-E beamline of sector-21(LS-CAT) at the Advanced Photon Source at Argonne National Laboratory. The observed reflections were reduced, merged, and scaled with DENZO and SCALEPACK in the HKL2000 package. The resolution cutoff is based on the criteria of l/sigma ratio = 2.0 in the highest resolution shell as guided by the HKL2000 package. Molecular replacements were performed by using the Collaborative Computational Project 4 (CCP4) program Phaser with the mammalian AMPK complex structure (PDB: 2Y94) and the human α2 kinase domain (PDB: 2H6D) as search models. Programs O and Coot were used to manually fit the protein models. Model refinement was performed with CNS and Phenix program package. All figures were prepared using PyMOL (DeLano Scientific). […]

Pipeline specifications

Software tools CCP4, Coot, CNS, PHENIX, PyMOL
Application Protein structure analysis
Organisms Homo sapiens
Diseases Diabetes Mellitus, Neoplasms
Chemicals Adenine Nucleotides, Ampicillin