Crystallographic Data Building

Structure Refinement. The refinement of the structure was based on an energy function approach (Brunger etal., 1987) arbitrary combinations of empirical and effective energy terms describing crystallographic data as implemented in XPLOR. Molecular model building was done on an IRIS Workstation (Silicon Graphics) with the software TOM, a version of FRODO (Jones, 1978). 

As a further example of a structure building exercise, consider the mineral diopside, CaMg-Si206, which was one of the first crystal structures to be determined, during the early years of X-ray crystallography. The crystallographic data is given in Table 5.12. 

In the absence of crystallographic data, drug designers channeled their energies into building models based upon deductions they could make from their SAR findings, incorporating stereochemical information as best they could. ... 

Consider a proposed mechanism and build a model, using crystallographic data if available, from the active site outwards. Choose important protein residues, substrates, intermediates and products, water molecules involved in the mechanism, etc., knowing that the validity of the results will depend critically on these choices. 

Overall, about two-thirds of the identities are found in sections covering about 20% of the peptide chain. Two of these sections include the aspartate residues that have been proposed to participate in the catalytic mechanism. A possible functional importance of the other sections is not yet known, but model building based on the x-ray crystallographic data may reveal the contribution of some of these sections to the stability of the tertiary structures of these enzymes. 

Many catalytically important oxide materials, such as ceria, are crystalline at (catalytic) operating temperatures and therefore a model of the crystal structure can be generated using symmetry operators. These symmetry operators, which have been introduced into many simulation codes (such as GULP), can be used to build the atomistic model using pertinent crystallographic data. This includes the... 

Theoretical studies associated with the crystallographic data might allow one to determine some rules for the association of structured fragments (i.e., for the formation of substructures such as supersecondary structures, and the assembly of these building blocks to form domains, and then the association of domains to form the globular compact structure of a protein). 

Figure 9.5 Building blocks and solid structures of luminescent coordination polymers derived from complex anions. Created using the Mercury 2.4 software from the crystallographic data in the respective articles (see text for references).

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