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Heavy-atom Substructure (heavy-atom + substructure)
Selected Abstracts5-Amino-2,4,6-tribromoisophthalic acid: the MAD triangle for experimental phasingACTA CRYSTALLOGRAPHICA SECTION C, Issue 5 2009Tobias Beck The title compound, C8H4Br3NO4, shows an extensive hydrogen-bond network. In the crystal structure, molecules are linked into chains by COO,H...O bonds, and pairs of chains are connected by additional COO,H...O bonds. This chain bundle shows stacking interactions and weak N,H...O hydrogen bonds with adjacent chain bundles. The three Br atoms present in the molecule form an equilateral triangle. This can be easily identified in the heavy-atom substructure when this compound is used as a heavy-atom derivative for experimental phasing of macromolecules. The title compound crystallizes as a nonmerohedral twin. [source] Features of the secondary structure of a protein molecule from powder diffraction dataACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Sebastian Basso Protein powder diffraction is shown to be suitable for obtaining de novo solutions to the phase problem at low resolution via phasing methods such as the isomorphous replacement method. Two heavy-atom derivatives (a gadolinium derivative and a holmium derivative) of the tetragonal form of hen egg-white lysozyme were crystallized at room temperature. Using synchrotron radiation, high-quality powder patterns were collected in which pH-induced anisotropic lattice-parameter changes were exploited in order to reduce the challenging and powder-specific problem of overlapping reflections. The phasing power of two heavy-atom derivatives in a multiple isomorphous replacement analysis enabled molecular structural information to be obtained up to approximately 5.3,Å resolution. At such a resolution, features of the secondary structure of the lysozyme molecule can be accurately located using programs dedicated to that effect. In addition, the quoted resolution is sufficient to determine the correct hand of the heavy-atom substructure which leads to an electron-density map representing the protein molecule of proper chirality. [source] The magic triangle goes MAD: experimental phasing with a bromine derivativeACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Tobias Beck Experimental phasing is an essential technique for the solution of macromolecular structures. Since many heavy-atom ion soaks suffer from nonspecific binding, a novel class of compounds has been developed that combines heavy atoms with functional groups for binding to proteins. The phasing tool 5-amino-2,4,6-tribromoisophthalic acid (B3C) contains three functional groups (two carboxylate groups and one amino group) that interact with proteins via hydrogen bonds. Three Br atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus readily identified in the heavy-atom substructure. B3C was incorporated into proteinase K and a multiwavelength anomalous dispersion (MAD) experiment at the Br,K edge was successfully carried out. Radiation damage to the bromine,carbon bond was investigated. A comparison with the phasing tool I3C that contains three I atoms for single-wavelength anomalous dispersion (SAD) phasing was also carried out. [source] With phases: how two wrongs can sometimes make a rightACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Pietro Roversi In isolation, both weak isomorphous/anomalous difference signals from heavy-atom derivatization and phases from partial molecular-replacement solutions for a subset of the asymmetric unit often fall short of producing interpretable electron-density maps. Phases generated from very partial molecular-replacement models (if generated carefully) can be used to reliably locate heavy-atom sites, even if the signal is not sufficiently strong to allow robust finding of the sites using Patterson interpretation or direct methods. Additional advantages are that using molecular-replacement phases to define the heavy-atom substructure avoids the need for subsequent hand determination and/or origin-choice reconciliation and that the partial model can be used to aid the mask determination during solvent flattening. Two case studies are presented in which it was only by combining experimental and molecular-replacement phasing approaches that the crystal structures could be determined. [source] | ||||||||||