Computational protocol: Myristoylation drives dimerization of matrix protein from mouse mammary tumor virus

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Protocol publication

[…] Diffraction data for phasing were collected using a 1.5 Å wavelength for native and iodide-soaked crystals. Data were collected to 1.9 Å resolution at 100 K for both datasets. The native dataset for the final structure was collected using a 0.9184 Å wavelength at 100 K. All datasets were collected at the MX14.2 beamline at BESSY, Berlin, Germany [], and processed using the XDS program []. The structure was solved with SHELXC/D/E programs [] using HKL2MAP GUI [] or GUI for SHELX programs []. Macromolecular phasing was performed according to the SIRAS method, using datasets from the native crystal and crystal soaked in potassium iodide (both measured using a 1.5 Å wavelength). The initial model was improved and rebuilt with the program Buccaneer []. This was followed by manual rebuilding with COOT [] and refinement with Refmac5 [] using the native dataset measured at 1.5 Å wavelength. At the end of this stage, the refinement statistics were as follows: R = 26.0 % (Rfree = 32.4 %). The final model, calculated from the dataset measured at 0.9184 Å wavelength, was refined to R = 22.6 % (Rfree = 26.3 %). The crystal parameters, data collection statistics, and refinement statistics are summarized in Table . […]

Pipeline specifications

Software tools XDS, SHELX, HKL2MAP, Buccaneer, Coot, REFMAC5
Applications Small-angle scattering, Protein structure analysis
Organisms Mouse mammary tumor virus, Human immunodeficiency virus 1
Diseases Neoplasms