title: Helical Symmetry of Nucleic Acids: Obstacle or Help in Structure Solution?
abstract: Crystallographic molecular replacement method is the key tool to define an atomic structure of nucleic acids. Frequently nucleic acids are packed forming continuous helices in the crystal. This arrangement of individual molecules in "infinite" pseudo helical structures in crystal may be the reason why the molecular replacement fails to find a unique position of the search atomic model as the method requires. The Patterson function, calculated as a Fourier series with diffraction intensities, has auxiliary peaks for such a molecular packing. Those near the origin peak indicate the orientation of the helices. The coordinates of other peaks are related to the molecular position and the rotation angle between two such "infinite" helices. Thus, the peak analysis allows getting molecular position even without a search model. An intelligent selecting and averaging of the phase sets corresponding to multiple probable positions of the search model again result in a unique solution but in the form of a Fourier synthesis and not a model. This synthesis can be used then to build an atomic model as it is the case for usual phasing methods.
authors.affiliation: Centre for Integrative Biology, Institute of Genetics and of Molecular and Cellular Biology, CNRS UMR 7104/INSERM U964/Université de Strasbourg, 1 rue Laurent Fries, Illkirch Graffenstaden, 67404, France, sacha@igbmc.fr.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Urzhumtsev
authors.forename: Ludmila
authors.initials: L
authors.lastname: Urzhumtseva
authors.forename: Ulrich
authors.initials: U
authors.lastname: Baumann
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D003460:Crystallization; D018360:Crystallography, X-Ray; D005583:Fourier Analysis; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D012996:Solutions
chemical_list: D009696:Nucleic Acids; D012996:Solutions; D012313:RNA