5. Describe quality of template(s)
Higher resolution structures are preferred if a choice can be made
between otherwise equally relevant structures. In the case of NMR
structures, use stereochemical and other quality estimates. The regions
most important for the intended use of the model should be reliably
determined. Although the descriptions of templates can be found from
articles and databases when using published structures, describe quality
measures relevant for your choice and model application. If template is
not published, even more specific descriptions are needed. In that case,
include also the coordinates and description of the structure
determination.
Sequence similarity and identity between the template and the protein to
be modelled protein sets limits for quality of the model. If several
related structures from different organism or for paralogs are
available, they can provide additional evidence for the modelled
structure.
Example. The template structure has been determined on high
resolution (1.45 Å) and it shows good quality parameters (e.g.
Rfree is 0.195). B values are low (<30) for
the functionally relevant substrate binding region and catalytic site
and secondary structural elements in the protein core. PROCHECK
(Laskowski et al., 1993) report did not indicate any quality issues.