Crystallographic techniques electron density maps

Crystallographers share the fruits of their work in the form of lists of atomic coordinates, which can be used to display and study the molecule with molecular graphics programs (Chapter 11). Less commonly, because fewer people have the resources to use them, crystallographers share the final structure factors, from which electron-density maps can be computed. The audience for structure factors includes other crystallographers developing new techniques of data handling, refinement, or map interpretation. 

Although crystallographical protein structures are firmly based on experimental data, it must be borne in mind that for resolutions of around 2 A and worse, the electron density maps are not sufficiently detailed to resolve individual atoms. In order to circumvent this problem, molecular modeling techniques are often applied and usually yield reliable structural models that best represent the measured diffraction patterns (25). However, the likelihood of... 

At this stage, assuming that the nominal resolution is 4 A or better, the electron density map should be of sufficient quality to interpret readily the course of the polypeptide chain and rapidly build a model, usually for the icosahederal asymmetric unit. Conventional crystallographic refinement techniques are then employed to refine the model against the observed data. 

In a recent publication (190), these techniques were applied to elucidate the crystal structure of low-dimensional compounds such as iron oxychloride, FeOCl, and its alkoxy substituents, FeOCl (OR), where R is Me or Et. It was shown that the local symmetry around the iron atom becomes higher for methoxy substituents compared to that for FeOCl. In fact, it is similar to that for y-FeOOH. Similarity of the one-dimensional electron density map along the c axis, obtained separately from X-ray crystallographic studies and from EXAFS fitting, reflects the reliability of the EXAFS fit and indicates its applicability to other two-dimensional systems with poor crystallinity. 

This process is similar to the decision making crystallographers use to interpret electron density maps main-chain tracing followed by side-chain modeling. The used techniques take many of the constraints and criteria into account that a crystallographer would apply, and the created model can be refined by a crystallographer. 

To elucidate a crystal structure, a crystallographer collects a set of observed diffraction intensities for a crystal diffracting in an X-ray beam. The intensities alone, however, are insufficient to construct a model the crystallographer needs to predict a set of unknowns called the reflection phases. These are initially estimated by various techniques to give a starting model. The starting model is then refined, and the refined model is used to recalculate the phases, allowing the calculation of an improved electron density map, which can be reinterpreted. The process is cyclical, but hopefully leads to an accurate interpretation of the reflection intensities. 

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