After an X-ray diffraction takes place some spots appear as two dimensional called refection? I am curious to know what do they actually represent? Is it an atom, group of atoms, a whole protein molecule or a group of protein molecule? And we ROTATE the crystal with various angle which is related with completeness. Now I am unable to understand what does completeness mean? Does anybody have some suggestion regarding this in very simple language?
A reflection represents the scattering of the entire unit cell at one diffraction angle. At any rotation of the crystal, there are multiple reflection conditions that result in scattering at different diffraction angles. In order to solve a structure you need to observe all possible reflection conditions.
You probably want to read a book on X-Crystallography or take a class.
Hi Prem,
The resulting "reflection" from a diffraction experiment arises from a complicated relation of the physics of the incoming photon wave interacting with each ordered lattice point in your crystal. If you look up topics like Bragg's law and the Ewald sphere construction that may aid in your understanding, as I think Stefan was alluding to.
So, each individual spot on the detector corresponds to many components of your crystal, and certainly not an individual protein, side chain, atom etc. (It is more to do with the internal order of the crystal and its relation to itself).
Also note that while what you see on your detector is a 2D spot, it is actually the result of a wave. The "third dimension", or phase, of the wave is not detected in the experiment and has to be obtained by comparison to previous structures (molecular replacement) or by introducing an atom in your protein that is heavy or special enough to alter the phase (SAD, MAD, MIR). This is the phase-problem in crystallography.
You should heed Stefan's advice and get a good book - start with something like "Crystallography Made Crystal Clear" and "Outline of Crystallography for Biologists".
Good luck!
I surely take your words Mr. Stefan. and I will go through the explanation given in the books. Thank you very much.
As with any math problem, do not get discouraged if the relationships of reciprocal and real space are not instantly clear. Spend the time to think things through and ask yourself questions. It might help your thinking to look at the crystallography and x-ray scattering review that got good responses on CCP4 (Putnam CD, Hammel M, Hura GL, Tainer JA "Solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution" Q Rev Biophys. 2007 Aug;40(3):191-285). You can download this from the SIBYLS website http://bl1231.als.lbl.gov under publications.
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