The higher resolution of the X-ray data usually results in a higher quality three-dimensional structure. For example, in the Ramachandran plot for the higher resolution structure on the image on the right, it is easy to see that the values of the torsion angles are clustered within the red regions (α- and β-regions). These are called allowed or energetically most favorable regions. Other regions are less favorable and are poorly populated in good-quality structures (yellow color). This results from a steric hindrance – specific rotations around the polypeptide chain will bring atoms too close to each other, creating high energy steric repulsion. For this reason, the Ramachandran plot serves as one of the critical indicators of the quality of a three-dimensional structure – a good quality structure is expected to have the majority, if not all, of its torsion angles within the allowed regions of the plot (image on the right).
However, sometimes we may find amino acids with "wrong" torsion angles, which may be for a good reason. The strain (high energy) created in a structure by such conformations may have functional significance (Pal & Chakrabarti, 2002
) and may even be conserved within a protein family!
Another exception from the principle of clustering around the α- and β-regions is provided by glycine. Glycine residues do not have a side chain, which allows a higher flexibility in regions of the polypeptide chain where G is located (usually loops, which explains the relatively high exposure of Gly in protein structures). As a result, the regions may adopt conformations that otherwise are forbidden. As mentioned earlier, proline, in contrast to glycine, fixes the torsion angles at a specific value, very close to that of an extended β-strand. A more detailed discussion of the quality of experimental structures can be found on the page on quality assessment