Electron density maps model building

Density map Model building - Modei Build and adjust a model in the electron ... 

Jones TA, Zou JY, Cowan SW, Kjeldegaard M. Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Cryst 1991 A47 110-9... 

The result is the electron density map of the protein crystal. The final task for the crystallographer is to build the appropriate protein model, i. e., putting amino acid for amino acid into the electron density. Routinely the theoretical amplitudes and phases are calculated from the model and compared to the experimental data in order to check the correctness of model building. The positions of the protein backbone and the amino acid side chains are well defined by X-ray structures at a... 

The crystallization and structural determination of the histone octamer was first reported in 1984 [34], However, the overall dimensions of the 3.3 A structure [15] did not appear to fit within the known X-ray structures of the nucleosome core particle [12,13], In an elegant analysis [16], re-examination of the original phasing of the histone octamer data revealed misplacement of the heavy atom site by 2.7 A. The structure was resolved, after which it was possible to build molecular models of the individual histones into the 3.1 A resolution electron density map of the histone core of the nucleosome [17]. Figure 2 shows the first atomic resolution model of the core histone octamer. Several additional publications followed in which the histone octamer structure formed the basis for constructing models of the NCP [17-21],... 

Model building is an interpretation of the currently available electron density. Refinement is the adjustment of the built model to fit better to the experimental data. A crucial point here is that a density map computed from the refined model is generally better than the map obtained from the same model before the refinement. This then allows for an even better model to be built. Thus, refinement is needed to improve the outcome of model building by generating a better electron density map and model building is needed to provide a model in the first place and to provide stereochemical restraints for the subsequent refinement to proceed smoothly. This viewpoint merges these two steps into one model optimization process. 

This chapter will address software systems to interactively fit molecular models to electron density maps and to analyse the resulting models. This chapter is heavily biased toward proteins, but the programs can also build nucleic acid models. First a brief review of molecular modelling and graphics is presented. Next, the best current and freely available programs are discussed with respect to their performance on common tasks. Finally, some views on the future of such software are given. 

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. 

We will now describe some details of the interpretation of the electron-density map that has been calculated. There are two major methods used in protein crystallography to build a model of the molecule from the various features found in an electron-density map. These methods differ from those used for small-molecules because the number of atoms is so large, and because individual atoms are not resolved in most protein crystal structures. A scheme, which is a continuation of Figure 8.10 (Chapter 8), is given in Figure 9.13. 

FIGURE 9.13. Building a model of a protein from an electron-density map. 

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