Crystallography structure solution

For many proteins, it is possible to generate structures of protein-ligand complexes quite rapidly. It is therefore not uncommon for many hundreds of structures to be determined in support of a drug discovery and optimization project. The major challenge for this level of throughput is informatics support. It is also this type of crystallography that is most in need of semiautomated procedures for structure solution and model building (see Section 12.6). 

The electron crystallography method (21) has been used to characterize three-dimensional structures of siliceous mesoporous catalyst materials, and the three-dimensional structural solutions of MCM-48 (mentioned above) and of SBA-1, -6, and -16. The method gives a unique structural solution through the Fourier sum of the three-dimensional structure factors, both amplitude and phases, obtained from Fourier analysis of a set of HRTEM images. The topological nature of the siliceous walls that define the pore structure of MCM-48 is shown in Fig. 28. 

The notion of a common core structure has been further supported by synchrotron X-ray fiber diffraction patterns of several amyloid fibrils the patterns show common reflections in addition to those at 4.7 and 10 A (Sunde et al., 1997). Although these data give some insight into the arrangement of the amyloid fibril core, the exact molecular structure and organization of the proteins making up this common core have yet to be uniquely defined. The inherently noncrystalline, insoluble nature of the fibrils makes their structures difficult to study via traditional techniques of X-ray crystallography and solution NMR. An impressive breadth of biochemical and biophysical techniques has therefore been employed to illuminate additional features of amyloid fibril structure. 

An emerging goal in the field of macromolecular crystallography methods development is the overall automation of the time-consuming steps in structure solution. To a large extent, two software packages exemplified that concept at the turn of the previous... 

The substitution of a different metal into an enzyme provides a very useful method for studying the immediate environment of the metal site. In addition to the use of Co2 for spectral studies, appropriate substitution allows the use of physical methods such as electron paramagnetic resonance (Co . Cu2 ). the Mdssbauer effect tFe2 ). proton magnetic resonance relaxation techniques (Mir ), or X-ray crystallography (with a heavy metal atom to aid in the structure solution). ... 

In modern crystallography virtually all structure solutions are obtained by direct methods. These procedures are based on the fact that each set of hkl planes in a crystal extends over all atomic sites. The phases of all diffraction maxima must therefore be related in a unique, but not obvious, way. Limited success towards establishing this pattern has been achieved by the use of mathematical inequalities and statistical methods to identify groups of reflections in fixed phase relationship. On incorporating these into multisolution numerical trial-and-error procedures tree structures of sufficient size to solve the complete phase problem can be constructed computationally. Software to solve even macromolecular crystal structures are now available. 

Chemists use a wide range of physical techniques for studying the structures and reactions of the molecules they are interested in. One of the skills they need is the ability to choose and exploit the most appropriate technique for studying the particular molecules of interest. X-ray crystallography is the ultimate arbiter of chemical structure and in many cases it is now the method of choice the use of automated data collection and direct methods of structure solution have reduced many problems to a routine level. However, crystallography has many limitations beyond the obvious need for crystals it cannot tell us anything about solutions, however pure they may be, or conformational equilibria, or complex mixtures or reaction kinetics. For this type of information, the chemist must turn to other physical techniques, such as some form of spectroscopy. 

Freeman CM, Gorman AM, Newsam JM (1997) Simulated annealing and structure solution. In Catlow CRA (ed) Computer modelling in inorganic crystallography. Academic, London... 

Dorset, D.L. (1996). Electron crystallography. Acto Crystallogr. B, 52,753-69. [112] Dorset, D., McCourt, M. R, Gao, L. and Voigt-martin, I. G. (1998). Electron crystallography of small molecules criteria for data collection and strategies for structure solution. J. Appl. Crystallogr., 31, 544-53. [112]... 

As with any protein simulation, the nature and limitations of the structural solutions for proteins provided by X-ray crystallography should always be borne in mind [125]. One obvious point is that hydrogen atoms are generally not observed because of their low electron density (neutron diffraction experiments can be useful to overcome this problem), and so it can be difficult to assign protonation states unambiguously, and to decide between possible rotamers or tautomers. This, and other factors such as model bias (for example in a molecular replacement solution), or simple error in construction of a model, may lead to the structural model being incomplete or incorrect in some places. 

C. J. Gilmore, K. Shankland and W. Dong, A maximum entropy approach to structure solution, in Structure determination from powder diffraction data. lUCr monographs on crystallography 13. W. I. F. David, K. Shankland, L.B. McCusker, and Ch. Baerlocher, Eds., Oxford University Press, Oxford, New York (2002). 

It is important to couple adsorption isotherm data with electron crystallography for the complete structural solution of mesoporous structures. Such methods when applied together offer accurate and reliable data that can be further used for the design and application of these complex structures. 

Typical X-ray diffraction experiments provide structure factor moduli, while the relative phases are lost. Recovery of the phase information is crucial for crystal structure solution and is referred to in crystallography as the phase problem. In single-crystal diffraction this problem is solved by different approaches ... 

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