Computational protocol: The structural basis for receptor recognition of human interleukin-18

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Protocol publication

[…] SAXS data of the IL-18/IL-18Rα/IL-18Rβ ternary complex were collected at the beamline 12ID-B of the Advanced Photon Source at Argonne National Laboratory (Argonne, IL, USA). The sample concentrations were 1, 3 and 5 mg−1 ml−1. The samples were run at 12 keV radiation energy, with a sample-to-detector distance of 2 m. The scattered X-rays were measured using a Pilatus 2 M detector. A flow cell was used to reduce radiation damage. Thirty images were taken for each blank and each sample.After background subtraction, the data were superimposed using Primus (). S is the momentum transfer equal to 4πsin(θ/2)/λ, where θ and λ are the scattering angle and X-ray wavelength, respectively. Rg is the radius of gyration, which was determined using the Guinier approximation of the data in the low s region (sRg<1.3), the linearity of which also served as an initial assessment of data quality (). The maximum particle dimension, Dmax, and the distance distribution function, P(r), were calculated using auto GNOM (). The low-resolution envelopes of the ternary complex were produced using DAMMIN by directly fitting the reciprocal space scattering profile. Fifteen DAMMIN models were generated and then aligned and averaged using DAMAVER and DAMFILT. Structural figures were prepared using Chimera. […]

Pipeline specifications

Software tools ATSAS, DAMMIN
Application Small-angle scattering
Organisms Homo sapiens