Talk:Resolution
From Proteopedia
Proposed revision for the portion of this article before the Contents, after discussion with Keiichi Namba. Comments welcome!
The resolution of a macromolecular crystal is the smallest distance between crystal lattice planes that is resolved in the diffraction pattern. Thus high numeric values of resolution, such as 4 Å, mean poor resolution, while low numeric values, such as 1.5 Å, mean good resolution. 2.05 Å is the median resolution for X-ray crystallographic results in the Protein Data Bank (88,701 on May 15, 2014).
The portion of the macromolecule that is best ordered in the crystal is responsible for diffraction spots that are farthest from the axis of the X-ray beam. Resolution is determined from these farthest spots based on their angle θ from the X-ray beam, using the Bragg equation solved for d:
d = λ / (2 sin θ)
where λ is the X-ray wavelength, and d is the smallest distance between crystal lattice planes that scatter discrete spots. The resolution is given by d.
If some portions of the macromolecule are less ordered in the crystal than others, these will have a poorer resolution. The "resolution of the crystal" represents the most ordered portions.
After an electron density map is calculated and refined with a fitted atomic model, an uncertainty of atomic position is calculated for each atom in the model. These single-atom uncertainties are called the B factors or temperature values of the atoms (see Temperature).
Cite: Explanation by Shigeta.
--Eric Martz 13:17, 15 May 2014 (IDT)
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/
