Phased rotation, conformation and translation function: performance with mononucleotides

A phased rotation, conformation and translation function (PRCTF) is a novel and promising tool for automatic model building in protein crystallography. Its performance has been tested on nucleic acid structures. A mononucleotide fragment of phosphate-to-phosphate type with seven conformation degrees of freedom was used as a search fragment. The position, orientation and internal torsion angles of all localized fragments are refined by a phased flexible refinement. In general, 50 to 93% of the fragments can be found by the PRCTF. Results depend on resolution and phase quality. The ability of the PRCTF to locate bases is significantly lower (3-30%), owing to the lack of heavy atoms. Individual localized fragments can be connected into polynucleotide chains.