Computational protocol: Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm

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Protocol publication

[…] The phases of the Cex1p crystals were determined from multiple anomalous diffraction data sets collected from a single crystal of selenomethionine-derivatized Cex1pΔC-SER, which diffracted up to 2.2 Å resolution. The peak data set was used to determine the locations of the selenium atoms, using the program SHELXC/D (). Several trials revealed 12 peaks among the 14 potential selenium sites expected in the asymmetric unit. Subsequent refinements of the heavy atom parameters and phase calculations were performed with the program SHARP (). The data collection and phasing statistics are shown in . The initial phases were improved by density modification with RESOLVE (). The initial model, containing 75% of all residues, was automatically built with RESOLVE. The model was further built manually using Coot (). The diffraction data set analysis using the program Phenix.xtriage () indicated that the crystal was pseudomerohedrally twinned with a twining fraction of 0.43. The structure was refined using the twin target function implemented in the program REFMAC5 (). The resulting twinning fraction was 0.425 for the twinning operator (−h, −k, h + l). Refinement statistics are provided in . […]

Pipeline specifications

Software tools SHELX, Coot, PHENIX, REFMAC5
Application Protein structure analysis
Organisms Saccharomyces cerevisiae