Practical Protein Chemistry - A. Darbre 1989

X-ray crystallography and electron microscopy
X-ray diffraction
Principles of structure determination in X-ray structural analysis

Before discussing the theoretical and methodological Features of X-ray crystallography, let us consider what kind of information can be obtained using this approach. X-ray Structure analysis of well-formed crystals of relatively small organic molecules makes it possible to calculate the electron density distribution within the crystal unit Cell. This distribution, also referred to as three-dimensional Fourier synthesis, can be represented as a series of two-dimensional contour maps corresponding to flat sections of the unit cell. The intervals between sections are chosen to be small enough so that the atoms forming the crystal unit cell appear as distinct, isolated maxima of electron density (Fig. 20.5). The resolution level of such maps, occasionally reaching 0.05 nm, allows the structure to be determined ab initio. Therefore, in A number of organic chemistry laboratories, The Use of X-ray crystallography to determine the Chemical Structure of compounds has already become routine practice (see, for example, [5]).

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FIG. 20.3. Schematic representation of a crystal consisting of regularly packed unit Cells. All cells are identical, and each is formed by one or more molecules. The regularity of packing causes the rays scattered by the crystal to concentrate into discrete, intense peaks.

In the case of large organic molecules, such as Proteins, electron density maps have a lower resolution (typically ~0.15 nm). As can be seen from Fig. 20.6, they do not allow individual atoms to be directly resolved. In such cases, determining the structure requires additional information, specifically the layout of covalent bonds within the molecule. This layout can be constructed based on the previously established Amino Acid Sequence of the polypeptide chain and data on their stereochemistry.

Figure 20.7 illustrates how, using such information derived from The Study of Amino Acids, a specific model of the backbone and side chains of a protein molecule can be constructed to fit the electron density map of the crystal unit cell.