Crystallographic Models

Simulated annealing A structure determination from diffraction data involves the development of an initial model, that is a structure solution step, and then completion and refinement of the model. Why are these steps distinct The answer is that today s structure refinement technology can operate effectively only when the starting model is relatively dose to the actual model crystallographic least squares techniques are unable to locate global... 

The original PDB file is a rich source of information for a modeler. Crystallographers do not intentionally include errors in structures often, there will be known issues in the structure, which the crystallographer will have reported. Crystallographers include REMARK records in PDB files that can inform the reader of this. 

Before one attempts to understand the chemistry of the crystallized macromolecule, one has to correct any errors in the initial atomic model. Crystallographic refinement can correct some of the errors, and can be formulated as a search for the global minimum of the target function ... 

Table 2 shows the results of our preliminary calculations of the pKa of the Cys403 residue, for several different models of the enzyme, based on two structures available from the PDB. In the case of the YPT structure, a crystal water molecule is close to Cys403 and was included in some of the calculations as part of the protein (i.e. it was treated with the same internal dielectric as that of the protein). Simulations denoted as -I-H2O in Table 2, include a crystallographically resolved, buried water molecule, situated 3.2lA from... 

The primary structure of a peptide is its ammo acid sequence We also speak of the secondary structure of a peptide that is the conformational relationship of nearest neighbor ammo acids with respect to each other On the basis of X ray crystallographic studies and careful examination of molecular models Linus Pauling and Robert B Corey of the California Institute of Technology showed that certain peptide conformations were more stable than others Two arrangements the a helix and the (5 sheet, stand out as... 

The structure proposed by Watson and Crick was modeled to fit crystallographic data obtained on a sample of the most common form of DNA called B DNA Other forms include A DNA which is similar to but more compact than B DNA and Z DNA which IS a left handed double helix... 

Protein Data Bank (Section 27 20) A central repository in which crystallographic coordinates for biological mole cules especially proteins are stored The data are accessi ble via the Worldwide Web and can be transformed into three dimensional images with appropriate molecular modeling software... 

Modeling and Crystallographic Studies of Estrogen Agonists and Antagonists... 

The comparison with experiment can be made at several levels. The first, and most common, is in the comparison of derived quantities that are not directly measurable, for example, a set of average crystal coordinates or a diffusion constant. A comparison at this level is convenient in that the quantities involved describe directly the structure and dynamics of the system. However, the obtainment of these quantities, from experiment and/or simulation, may require approximation and model-dependent data analysis. For example, to obtain experimentally a set of average crystallographic coordinates, a physical model to interpret an electron density map must be imposed. To avoid these problems the comparison can be made at the level of the measured quantities themselves, such as diffraction intensities or dynamic structure factors. A comparison at this level still involves some approximation. For example, background corrections have to made in the experimental data reduction. However, fewer approximations are necessary for the structure and dynamics of the sample itself, and comparison with experiment is normally more direct. This approach requires a little more work on the part of the computer simulation team, because methods for calculating experimental intensities from simulation configurations must be developed. The comparisons made here are of experimentally measurable quantities. 

Deisenhofer, J. Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9 and 2.8 A resolution. Biochemistry 20 2361-2369, 1981. 

One must be sure of the purity of the model compound. It may have deteriorated (for example, by reaction or water absorption), its surface may not have the same composition as the bulk, or it may not be of the correct crystallographic phase. It is tempting to use single crystals to be sure of the geometric structure, but noncubic crystals give angle-dependent spectra. The crystallography of any compound should be checked with XRD. 

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