Acta Crystallographica Section D: Biological crystallography appreciates the presentation of articles covering any aspect of structural biology, with special emphasis on the structures of biological macromolecules and the methods used to determine them. Reports on new protein structures, like structure-function articles which could include crystallographic binding studies or structural analysis of mutants or other modified forms of a known protein structure.
The key criterion is that such items must present new knowledge about biology, chemistry or structure. Articles on crystallographic methods should be geared towards biological crystallography and may include new approaches to any aspect of the determination or analysis of structures. Articles on the crystallization of biological molecules will be accepted as long as they focus on new methods or other characteristics that are of general importance or applicability.
Molecular substitution phase remains difficult for targets that are far from the search model or in situations where the the crystal diffracts only weakly or with low resolution. Here the process of determination and improvement of the structure of Cgl1109, a putative succinyl diaminopimelate desuccinylase from Corynebacterium glutamicum, at a resolution of 3 A˚ is described using a combination of homology modeling with MODELLER, molecular substitution phase with Phaser, refinement of the deformable elastic network (DEN) and automated model building using AutoBuild in a semi-automated way,followed by final refinement cycles with phenix.refine and Coot.
This difficult case of molecular replacement illustrates the power to include DEN constraints derived from a boot model to guide the movements of the model during refinement. Resulting improved model phases provide a better start points for automated model building and producing more significant difference peaks in anomalous Fourier difference maps to locate anomalous scatterers than standard ones refinement. This example also illustrates a current limitation automated procedures that require manual adjustment of Local sequence misalignments between the homology model and the target sequence.