Fitted electron density

Final structure Fit electron density Solve structure Collect diffraction data Figure 12.1 The crystallographic pipeline. 

Amat, L. and Carbo-Dorca, R. (1999) Fitted electronic density functions from H to Rn for use in quantum similarity measures cis-diamminedichloroplatinum(II) complex as an application example. 

The question of the oxidation state of the heme iron with NO bound might in principle thought to be accessible by consideration of the Fe-N distance and bond angles. However, with respect to distance it is important to realize that X-ray structures do not in themselves determine distances such as that from Fe to N to sub-angstrom resolution. The procedure is to fit electron density using restraints frequently obtained from small molecule studies. Thus, unless the resolution of a protein... 

Quantum Chemical to Phenomenological Approaches, R. Carbo, Ed., Kluwer Academic Publishers, Dordrecht, The Netherlands, 1995, pp. 89-111. General Suggestions and Applications of Quantum Molecular Similarity Measures from Ab Initio Fitted Electron Densities. 

Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skill which usually takes several years to acquire. 

Molecular volumes are usually computed by a nonquantum mechanical method, which integrates the area inside a van der Waals or Connolly surface of some sort. Alternatively, molecular volume can be determined by choosing an isosurface of the electron density and determining the volume inside of that surface. Thus, one could find the isosurface that contains a certain percentage of the electron density. These properties are important due to their relationship to certain applications, such as determining whether a molecule will fit in the active site of an enzyme, predicting liquid densities, and determining the cavity size for solvation calculations. 

BL Sibanda, TL Blundell, JM Thornton. Conformation of (I-hairpms m protein stractures A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 206 759-777, 1989. 

From a map at low resolution (5 A or higher) one can obtain the shape of the molecule and sometimes identify a-helical regions as rods of electron density. At medium resolution (around 3 A) it is usually possible to trace the path of the polypeptide chain and to fit a known amino acid sequence into the map. At this resolution it should be possible to distinguish the density of an alanine side chain from that of a leucine, whereas at 4 A resolution there is little side chain detail. Gross features of functionally important aspects of a structure usually can be deduced at 3 A resolution, including the identification of active-site residues. At 2 A resolution details are sufficiently well resolved in the map to decide between a leucine and an isoleucine side chain, and at 1 A resolution one sees atoms as discrete balls of density. However, the structures of only a few small proteins have been determined to such high resolution. 

Figure 18.12 The electron-density map is interpreted by fitting into it pieces of a polypeptide chain with known stereochemistry such as peptide groups and phenyl rings. The electron density (blue) is displayed on a graphics screen in combination with a part of the polypeptide chain (red) in an arbitrary orientation (a). The units of the polypeptide chain can then be rotated and translated relative to the electron density until a good fit is obtained (b). Notice that individual atoms are not resolved in such electron densities, there are instead lumps of density corresponding to groups of atoms. [Adapted from A. Jones Methods Enzym. (eds. H.W. Wyckoff, C.H. Hirs, and S.N. Timasheff) 115B 162, New York Academic Press, 1985.]...

Nevertheless, the formal A/ scaling has spawned approaches which reduce the dependence to A/. This may be achieved by fitting the electron density to a linear combination of functions, and using the fitted density in evaluating the J integrals in the Coulomb term. 

In recent years, high-resolution x-ray diffraction has become a powerful method for studying layered strnctnres, films, interfaces, and surfaces. X-ray reflectivity involves the measurement of the angnlar dependence of the intensity of the x-ray beam reflected by planar interfaces. If there are multiple interfaces, interference between the reflected x-rays at the interfaces prodnces a series of minima and maxima, which allow determination of the thickness of the film. More detailed information about the film can be obtained by fitting the reflectivity curve to a model of the electron density profile. Usually, x-ray reflectivity scans are performed with a synchrotron light source. As with ellipsometry, x-ray reflectivity provides good vertical resolution [14,20] but poor lateral resolution, which is limited by the size of the probing beam, usually several tens of micrometers. 

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