Tuesday, October 23, 2018

biochemistry - What is Cβ (C-beta) deviation?


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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periodic trends - Comparing radii in lithium, beryllium, magnesium, aluminium and sodium ions

Apparently the of last four, $\ce{Mg^2+}$ is closest in radius to $\ce{Li+}$. Is this true, and if so, why would a whole larger shell ($\ce{...