Computational protocol: Structural study of MCPIP1 N-terminal conserved domain reveals a PIN-like RNase

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Protocol publication

[…] Native NCD and Se-derived crystal diffraction data sets were collected at BL-17 A, Photon factory, KEK, Japan. The wavelength used for anomalous diffraction data collection was 0.9790 Å. Native NCD-ZF crystal diffraction data was collected at BL-17I, SSRF, China. All data sets were processed and scaled using the HKL2000 package (). Due to anisotropic diffraction of NCD-ZF crystal, the ellipsoidal truncation and anisotropic scaling was applied to NCD-ZF data using the online Diffraction Anisotropy Server (). The phasing of the NCD structure was solved using the Single-wavelength Anomalous Diffraction (SAD) method with the hkl2map program (). The NCD-ZF structure was solved by the Molecular Replacement (MR) method using the NCD structure as a model (,). Mg2+-derived NCD crystals were obtained by soaking the NCD crystal in a reservoir containing 15 mM MgCl2. Mg2+-derived crystal data was collected at BL-17A, Photon factory, KEK, Japan. The Mg2+ ion-containing structure was solved by the MR method using the NCD structure as a model. All refinements were carried out using the Phenix.refine and Coot programs (,). shows the crystallographic data and refinement statistics for the two structures. Figures were prepared using PyMol (). […]

Pipeline specifications

Software tools HKL2MAP, PHENIX, Coot, PyMOL
Application Protein structure analysis