Bulk electron-density maps

The electron density distribution for solvent molecules can be improved if the contribution from bulk water to the X-ray scattering is included in the model. This affects the low-angle j X-ray intensity data which are omitted in early stages of the least-squares refinement of protein crystal structures. If they are included in refinement and properly accounted for, the signal-to-noise ratio in the electron density maps is significantly improved and the interpretation of solvent sites is less ambiguous. 

There are two ways for including the contribution from bulk water. One was first introduced in fiber diffraction analysis of polynucleotides. It subtracts the X-ray scattering contribution of bulk water from the individual atomic scattering factors used in the structure analysis [700,836], The other incorporates the continuous electron density of liquid water, 0.34 e/A3, in the electron density calculations. As a result the more localized solvent atoms are I more clearly defined in difference electron density maps [837]. 

Bovine heart cytochrome c oxidase is in a dimer state in the asymmetric unit of the crystal as shown in Fig. 7 (see color insert) (Tsukihara et al., 1996). Thirteen different subunits were identified in each monomer in the X-ray structure of the fully oxidized enzyme at 2.8-A resolution. The top view from the intermembrane side indicates a fairly strong interaction between the two monomers. The middle portion of the side view is readily identified as the transmembrane region by the large cluster of a-helices. This part was composed mainly of 28 a-helices as had been predicted by the amino acid sequences. The Ga backbone traces show that most of the a-helices are not arranged stricdy perpendicularly to the membrane surfaces, in contrast to the prediction by the amino acid sequences. Thus, most of a-helices in the X-ray structure are longer than those predicted by the amino acid sequences. The three largest subunits, subunits I, II, and III, form a core portion and the other 10 nuclear-encoded subunits surround the core as shown in Figs. 7C and 7D. In the X-ray structure at 2.8-A resolution, 3560 of 3606 amino acid residues were identified in the asymmetric unit composed of a dimer. Only 23 of 1803 amino acid residues per monomer were not detectable in the electron density map. Most of the undetectable residues are in the N- and C-terminals, which are exposed to the bulk water phase. 

All theoretical studies agree with this second picture [13-17,39,99]. This is shown by the plots of the electron density maps and in particular by density difference maps which show very clearly the electron localization at the center of the vacancy [39,55]. This is true not only for the bulk but also for the surface of MgO, Fig. 5. The localization of the electrons in the center of the vacancy is an indirect proof of the highly ionic nature of MgO. In fact, the electrons are trapped in the cavity by the crystalline Madelung potential. Calculations performed on cluster models have shown that in absence of the external field the electrons tend to distribute more over the 3s levels of the Mg ions around the vacancy [38]. The localization of the electron in the center of the vacancy is... 

Thus Fig. 1 shows a section through the three-dimensional electron density map in the plane of the CO, Cl, and O groups. Clearly, the CO and Cl replace one another at random. This presumably is the result of molecular oxygen attacking the parent square-planar compound from either side. If then the tri-phenylphosphine ligands are equivalent in solution, and are of sufficient bulk to control the packing, such disorder is not unexpected. The final refinement... 

Fig. 9.9. Electron-density maps obtained for CU2O on a (110) plane, [622]. (a) Total electron density, (b) Density difference maps, bulk minus neutral atom superposition. Values corresponding to neighboring isodensity lines differ by 0.01 e/Bohr . The full and broken curves in (b) indicate density increase and decrease, respectively.

Pig. 10.4. Two-dimensional (2D) difference electron-density maps (the total density in the perfect SrTiOa bulk minus the sum of electron densities of both isolated oxygen atoms and defective SrTiOs) projected onto the (110) section plane PP for 80-atom (a) and 270-atom (b) fee superceUs containing a single oxygen vacancy [732]. Dash-dot isolines correspond to the zero level. Sohd and dashed isolines describe positive and negative values of electron density, respectively. The isodensity increment is 0.002 e/A . 

Figure 8.26 (a) Difference electronic charge density map (calculated bulk minus isolated ion densities), displayed in the crystallographic plane containing the central Mo and the vertices 0(1)0(2 )0(3 )0(2) of one isolated MoOs octahedron. Continuous, dashed and dot-dashed lines correspond to positive, negative and zero difference respectively. The interval between the isodensity lines is 0.005 a.u. (electrons ao ). 

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