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Molprobity and some other protein structure validation tools report a Cβ deviation statistic and offer plots for it (example below). Apparently if the Cβ is greater than 0.25 Å, some attention should be given to the residue.

The statistic is given in units of angstroms, but I'm not sure what it's actually referring to. With the Rama plot, it's the peptide dihedral angles, but what is this? And why are the graphs 2-D despite the one dimension given?

example C-beta graph

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  • $\begingroup$ This is a protein-specific parameter, or? I'm guessing this from the context, but it might be useful to make this explicit in the question. $\endgroup$ – Mad Scientist May 22 '12 at 19:52
  • $\begingroup$ @MadScientist yes, I mention that "protein structure validation tools report" this; do you mean edit the title? $\endgroup$ – Nick T May 22 '12 at 20:43
  • $\begingroup$ I just missed that part somehow, it's fine like it is. $\endgroup$ – Mad Scientist May 23 '12 at 5:49
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Just browsing through this "Unanswered Question" now (in late 2014). I hope it's not too late?

In protein structure validation, Ramachandran outliers are a strong, but not absolute, indicator that the backbone confirmation of your protein structure deviates from all the high resolution structures known to date, and hence need your attention during the progress of refinement.

If all the phi-psi angles (backbone conformation) all fall into the "allowed/favoured" regions on the Ramachandran plot, your structure model is probably, but not necessarily, esp in the case of low resolution, correct. Hence there are other weaker criteria in protein structure validation, and Cbeta deviation is just one of them. In the light of high resolution structures out there, it turns out that Cbeta also has a favoured range of dihedral angles, suggesting that any misfit between your structure and the "probable" side chain-backbone conformation also deserves your attention during structure refinement.

In MolProbity, the justification and validation procedure are described here.

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