Computational protocol: Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling

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Protocol publication

[…] Solutions of SL1067 were heated to 95 °C for 10 min and then snap-cooled on ice. To make the IL-1α/SL1067 complex, IL-1α and SL1067 were mixed at a 1:1.1 ratio, in which the final protein concentration was 12 mg ml−1. Crystals of the complex were grown by mixing equal volumes of precipitating solution (0.2 M NaCl, 0.1 M Na acetate, and 22% polyethylene glycol 8000). Crystals were cubic shaped and grew to full size in 2 days. After removal from the drops, crystals were flash frozen with liquid nitrogen. Diffraction data were collected at NE-CAT beamline ID-24 at the Advanced Photon Source (Argonne National Laboratory, Argonne, IL, USA). Integration, scaling and merging of the intensities were carried out with the program imosflm and SCALA from the CCP4 software suite. [...] The structure of IL-1α was solved by molecular replacement with the available IL-1α PDB coordinates (PDB ID 2ILA, with only alpha-C atoms) for the search model using Phaser in the CCP4 software suite. The model was built with Autobuild in the Phenix suite. The SL1067 section of the model was fit and built manually using the Rcrane plugin within Coot. Refinement cycles were performed using Refine in Phenix, alternating with iterative manual rebuilding in Coot. A summary of data collection and structure refinement statistics is given in Table . […]

Pipeline specifications

Software tools iMosflm, CCP4, PHENIX, Coot
Applications Small-angle scattering, Protein structure analysis
Chemicals Hydrogen, Sodium