When solving the phase problem in x-ray crystallography using the heavy atom isomorphic replacement method, we cannot calculate the patterson function for the protein structure factor and instead calculate it for the heavy atom structure factor. However, why is it that we can calculate the patterson function for the protein structure factor without problems in the molecular replacement method?
Dear Jane, as a synthetic chemist I'm not an expert enough to give you a qualified answer to your interesting technical question. However, I just came across the following potentially useful article which might help you in your analysis:
An introduction to molecular replacement
Article An introduction to molecular replacement
Fortunately this article has been posted by the authors as public full text on RG. Thus you can freely download the pdf file.
Good luck with your research and best wishes!
Dear Jane,
I don't know if I totally understand your question.
The Patterson function is a Fourier transform of a set of squared reflection amplitudes. The "catch" here is that those squared reflections are not-phased. So, in practical terms, this means that you can calculate the Patterson function for any diffraction data set because these squared amplitude values are proportional to the diffracted intensities (any X-ray Crystallography review or book will show you the math behind this).
So, why do you mean you cannot calculate from a SIR or SIRAS experiment? Is it because you assume that the Friedel's Law gets broken at anomalous scattering wavelength maxima? Can you please elaborate a bit on your statement?
Best regards,
Jose
Check https://www.sciencedirect.com/topics/chemistry/molecular-replacement
Also check http://www.bioinfo.rpi.edu/bystrc/courses/bcbp4870/lecture5.pdf
Hello Jane,
Check this paper
https://www.ou.edu/cas/chemistry/xray/solve
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