I am wondering if it is possible to find the local resolution of a crystal structure. Usually, the resolution of the PDB is assigned the resolution of the highest resolved part of the protein/nucleic acid. However, it is actually a range of resolution (ie. 2-8 A). I am wondering if it possible to extract the resolution of each atom from a PDB file?
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$\begingroup$ If you look at the PDB file, there is a range of resolution. This makes sense because different regions are resolved at different resolutions. Please see below: REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 $\endgroup$– AstronomerNov 28, 2017 at 21:24
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$\begingroup$ Ah, do you actually want the temperature? proteopedia.org/wiki/index.php/Temperature $\endgroup$– gilleainNov 29, 2017 at 9:42
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$\begingroup$ @gilleain I am aware of the B-factor, but it seems that it is not directly related to the resolution of the macromolecule. Would a larger B-factor necessarily mean a lower resolution? I always thought B-factor was the local flexibility of an atom. $\endgroup$– AstronomerNov 29, 2017 at 21:56
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$\begingroup$ @wanlei I think it's the best you can get. Also B-factor is the uncertainty, so a high B-factor certainly means lower resolution. $\endgroup$– gilleainNov 30, 2017 at 11:03
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$\begingroup$ It's not directly related since higher uncertainty could come from sidechain flexibility. $\endgroup$– AstronomerDec 18, 2017 at 22:31
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The question has false statements:
Usually, the resolution of the PDB is assigned the resolution of the highest resolved part of the protein/nucleic acid.
Usually (in ~90% of the PDB entries) the experimental method used is X-ray crystallography. In such case the resolution refers to a distance between crystal lattice planes: it is assigned the value of the smallest distance between lattice planes that was resolved in the diffraction pattern.
Crystallographic experiment measures reflection. Each reflection corresponds to a set of lattice planes in the crystal. The spacing between these planes, d, is the measure of resolution. "Resolution range 3 - 20 Angstroms" means that the reflections used in the refinement had d between 3 and 20 Angstroms.
The resolution is simply dmin - the smallest distance between crystal lattice planes that resulted in a reflection usable in the refinement. Each reflection contributes to each point in the electron density map, so while we can talk about local quality of the structure, the resolution cannot be local.
Unless the data comes from a Cryo-EM experiment, where the resolution is defined differently and people can talk about local resolution.
