Talk:Resolution
From Proteopedia
Some rough notes added below for potential incorperation into the article (delete below when added ;-)
- --Dan Bolser 12:08, 4 January 2009 (IST)
Post to PDB-L
Some time back I remember reading a posting to this list where some very general rules-of-thumb were given for interpreting the value of the resolution of an X-ray structure.
The rules were something like (very approximate version!)
- >4 Angstrom = Unlikely to even get backbone right (anything goes).
- >3 Angstrom = Backbone possible but side chain orientation is probably wrong.
- >2 Angstrom = Sidechain orientation is broadly correct, but 'some other problems' exist.
- >1 Angstrom = 'Some other problems' are probably gone.
- >0.5 Angstrom = Hydrogen atoms are 'visible'.
Where (if I remember correctly) the 'some other problems' were issues of sterio-chemistry, orientation of specific groups, etc.
Please note, if I remembered incorrectly the above 'rules' may be totally wrong!
Reply
I would refer you to a very nice talk Greg Warren (at Openeye) gave at the ACS meeting.
In this presentation he gave multiple examples of problematic situations many of us have seen. The bottom line is that even with apparently high resolution (<2A) many serious problems can remain due to poorly fit density, missing local density, multiple solutions to the fit, and especially ligand issues.
At least as important as resolution is Rfree, which gives you a measure of how well the model structure fits the electron density generated from structure factors (the actual experimental data).
In a general sense the table you cite is not too bad I suppose, but the problem is that there is not a general answer. A very good structure might be bad where it matters to you, and a low resolution structure, say 3A, might not be as bad as you think.
Dominic Ryan
Reply
I would also add that "quality" is not something that depends solely on resolution, but also very heavily on the environment of the residue. At 2.8A to 3A resolution, for example, it's still possible to determine the orientation of buried residues, but things may be really ugly on the surface. So, if what you want is have a measure about "what to trust" in a x-ray structure, it's a good idea to check the real-space correlation by residue (a coeficient that tells how well the modeled structure fits in the electron density), or visually check what's going on using the electron density server at http://eds.bmc.uu.se/eds/
