Hi Everyone:
When I analyze a protein crystal structure from the PDB using Ramachandran plot. It has some outliers, i.e. 10 or so. I would expect that all amino acid residues on a non-theoretical protein to have favorable/allowable psi and pi angles. What could contribute to the outliers I observed on the protein structure? Thank you for the answer.
Hi Yang Zhang
Having outliers doesn't directly mean that your model is bad or anything. Even for non-theoretical proteins (i.e., obtained from crystallography, NMR, etc), their structure can still present some outliers. If you are planning to submit your structure to a Molecular Dynamics analysis (at least 10ns), it is quite possible that, in the end, your model will show fewer outliers, as Zhaoxi Sun mentioned before.
Outliers are common since they are also a result from the experimental procedures, equipment and even the nature of your protein. Some proteins have highly Intrinsically Disordered Regions (IDR) that usually lead to outliers (yes, even after equilibration and minimization). I advise you to be familiar with the nature of your protein, instead of only looking at the analytical side of the equation.
Cheers.
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