Macromolecular structural model

A macromolecular structural model is a representation of the three-dimensional organization of a biological macromolecule or complex. It can include atom identities, coordinates, crystallographic site occupancy, atomic displacement parameters and alternative conformations. A deposited coordinate set is an interpreted model supported by measurements, rather than the measurements themselves.^[ref]

For X-ray crystallography, an electron density map constrains where atoms can be placed, while chemical geometry and experimental uncertainty constrain interpretation. Poorly resolved regions can remain absent from the model or be represented less precisely. A numerical coordinate printed to several decimal places does not establish equally fine positional accuracy.

An original coordinate comparison illustrates the distinction. Suppose two models place the same atom at $(0,0,0)$ and $(0.2,0,0)$ in angstrom units. Their separation is $0.2\mathring{\mathrm{A}}$, but that number alone cannot say which model is better. One must examine agreement with the data and the relevant uncertainty, not merely the number of digits or the difference between the coordinates.

A concrete example is calmodulin structure1CLL in the Protein Data Bank. The record contains a refined model with four calcium ions, while its primary citation describes poorly defined terminal residues. Both the observed binding environment and the unresolved regions are part of interpreting the structure.^[ref]

Structural claims should therefore specify which components and conformations are modeled, what experiment supports them and what remains unresolved. A model useful for one question does not automatically establish the complete dynamics or every biochemical activity of the molecule.