How can atomic RMS differences / atomic RMS distributions help us understand the structure of a protein?

Question

[Inesgomes9586]

For example, I have a paper that says: "the atomic RMS distribution about the mean coordinate positions is 0.41 +/- 0.04 A for the backbone atoms and 0.82 +/- 0.04 A for all atoms" And I have no idea what any of this means, I found several papers with this kind of information but none of them explain why this is relevant in order to understand the structure of a protein and I haven't learned anything about NMR yet so I'm very confused and curious haha.

[Joe]

The ELI5 for this would be: big RMSD bad, low RMSD good.

Answer 1

[jgreener]

The RMSD measures how similar two conformations of a protein are, for example a model and the native structure. See https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions.

After superimposing the two structures, the RMSD is 0 Angstrom if the conformations are identical or higher if the paired atoms are further apart.

It can be used for many things, such as assessing the quality of a model or monitoring conformational change during a molecular dynamics simulation.