Idealized atomic coordinates of yeast phenylalanine transfer RNA.

The atomic coordinates are given for yeast phenylalanine transfer RNA in the orthorhombic crystal form. The structure has been refined by fitting to successively improved electron density maps at 2.7 8 resolution. The model fitting has been accomplished by using an interactive computer graphics system to minimize the errors inherent in manual model building and coordinate measurements, using an optical comparator. The atomic coordinates have then been "idealized" to make bond distances, bond angles, steric conformation and non-bonded contacts close to standard values, while constraining the model to fit the electron density maps. The three dimensional structure of yeast phenylalanine tRNA (tRNA PHE . ) In the orthorhombic crystal form has been determined by X-ray crystallographic methods. The backbone structure of the molecule was determined at 4 8 resolution by the multiple isomorphous replacement method (l), and the tertiary hydrogen bonding scheme between the bases has since been described for the PHE yeast tRNA in the orthorhombic (2) and the monoclinic crystal form (3), based on the electron density maps at 3 8 resolution. The refinement for the yeast PHE tRNA structure in the orthorhombic crystal form has been pursued along two different directions, one at M.I.T. (to be submitted to this journal), and the other at Duke University. We present the results from the latter approach here. In fitting the models to successively improved electron density maps obtained by the "partial structure fourier method" (4), we have used initially an optical comparator (5), then an interactive computer graphics system developed in collaboration with the Department of Computer Science at the University of North Carolina at Chapel Hill. The "idealization" was achieved by the use of a program written by Hermans and McQueen (6), and modified for nucleic acid structures by Sussman (4). The idealization is accomplished by minimizing a criterion function for each atom sequentially in the structure. This function contains terms for deviations from standard bond angles, bond Vol. 68, No. 1, 1976