November 2003 issue
Proceedings of the CCP4 study weekend
Cover illustration: Elastase molecule showing bound iodide and polyiodides as blue spehres, p. 1923.
CCP4 study weekend
Seven gadolinium complexes used as highly concentrated solutions for co-crystallization or soaking experiments are shown to be a very powerful tool for obtaining heavy-atom derivatives for macromolecular structure determination. SAD phasing experiments have successfully been carried out with several proteins of known structure, as well as with a 450 kDa protein assembly of previously unknown structure.
The procedures for preparing triiodide derivatives are described and examples of SAD and SIRAS phasing for six test proteins using conventional and synchrotron sources are presented.
The lack of noble-gas binding sites in native proteins has been addressed by introducing new sites using protein engineering. In addition to facilitating phase determination, these sites may also prove invaluable during model building and molecular replacement.
Methods used to obtain experimental phases and ways of optimizing these experiments are described.
The use of Cr Kα radiation combined with other advances in hardware and software makes sulfur SAD phasing of protein diffraction data rioutinely achievable in the home laboratory.
An overview of Patterson methods and direct methods is presented. This is followed by an outline of a new hybrid substructure search.
The extracellular domain of the LDL receptor, a medium-sized protein with 700 residues, was determined from multiple non-isomorphous crystals at low resolution in a MAD experiment by exploiting the anomalous signal from two and a half 12-tungstophosphate clusters present in the asymmetric unit. A case study is presented.
The accuracy of Se substructures obtained by different routes using SHELXD is assessed by comparing substructure solutions with the selenium positions in the refined models.
A twinned crystal is an aggregate in which different domains are joined together according to a specific symmetry operation: the twin law. Reflections from different domains may overlap and twinned crystals fall broadly into two categories in which either all reflections or only certain zones of reflections are affected by overlap. The former occurs when a crystal lattice belongs to a higher point group than the crystal structure itself; the latter frequently occurs when the twin law is a symmetry operation belonging to a higher symmetry supercell.
Successive formulations of experimental phasing methodology are reviewed from a historical and conceptual perspective, including the latest developments in SHARP. An improved method for encoding and exploiting phase information in the complex plane is presented. Directions for further research are indicated.
A discussion of the types of measurement errors, their estimates and their consequences in further stages of the crystallographic process is presented.