Open AccessA general method for phasing novel complex RNA crystal structures without heavy‐atom derivatives
Author(s) -
Robertson Michael P.,
Scott William G.
Publication year - 2008
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444908011578
Subject(s) - ribozyme , phaser , rna , multiple isomorphous replacement , crystal structure , phase problem , crystallography , anomalous scattering , hairpin ribozyme , chemistry , physics , scattering , quantum mechanics , biochemistry , gene , peptide sequence , optics , diffraction
The crystallographic phase problem [Muirhead & Perutz (1963), Nature (London) , 199 , 633–638] remains the single major impediment to obtaining a three‐dimensional structure of a macromolecule once suitable crystals have been obtained. Recently, it was found that it was possible to solve the structure of a 142‐nucleotide L1 ligase ribozyme heterodimer that possesses no noncrystallographic symmetry without heavy‐atom derivatives, anomalous scattering atoms or other modifications and without a model of the tertiary structure of the ribozyme [Robertson & Scott (2007), Science , 315 , 1549–1553]. Using idealized known RNA secondary‐structural fragments such as A‐form helices and GNRA tetraloops in an iterative molecular‐replacement procedure, it was possible to obtain an estimated phase set that, when subjected to solvent flattening, yielded an interpretable electron‐density map with minimized model bias, allowing the tertiary structure of the ribozyme to be solved. This approach has also proven successful with other ribozymes, structured RNAs and RNA–protein complexes.