Is it customary for investigators to publish the original x-ray diffraction data used in macromolecular structural determination? If not, why not; and if so, is there an online database where these data may be downloaded?


1 Answer 1


In many cases they are available. One of the establishing principles of the Protein Data Bank (PDB) was to store not only the models (atomic positions and identities) of macromolecules and proteins, but also the originating X-ray data, more recently in structure factors.

If the question is 'why are they giving only the structure factors and not the original data they took' - such a task would require a lot of curation effort for very little scientific benefit. Scaling the individual sets of data from the detector used to be a bear of a task. The original myoglobin structure would entail scanned films in an ancient format from the 50s. Nobody would be able to use that now without hacking the image format, if it wasn't on paper tape or cards. In fact in that case the structure factors are not available. Scaling many or several data collections together was often done with custom tweaks into the 70s and then in the 90s data collection became more routine, but several generations of x-ray detectors became popular and then faded from the market. Each had its own eccentricities and requirements for combining data sets from multiple reads.

The purpose of having structure factors available is to allow anyone to reconstruct the electron density and evaluate the interpretive act which is tracing a peptide through electron density. Since that format is mainly independent of the detector and has been fairly consistent over the years, it delivers a significant amount of scientific bang for the buck.

If you want raw image data or detector-proprietary data before multiple data sets from different crystals before they were combined you will have to contact the authors, who would probably have to sift through a sea of DVDs to get to it. In older cases it might be tapes.

So as far as Structure factors, which are essentially the square root value of the combined and scaled Intensity data, they are available and a part of every submission to the pdb:

Look on any X-ray Structure Page at RCSB. For example this one.

There is a box called "Experimental Details" and you can download the structure factors there by clicking a link.

If you are looking for more than one at a time, there are bulk downloads available through their download page. Check the "Structure Factors" box. Raw intensity data should be available if you look around for it as well.

Further Suggestion: I was thinking that if you look at the scaling software that comes with the X-ray detectors you might find some tutorials with unscaled raw data. I found one example at Marresearch - hen egg white lysozyme.

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    $\begingroup$ let me misuse this comment to bring your attention to crystallography.SE proposal. We don't know if it will gather enough people to make it worth its own site, although such site could be helpful. Now some relevant questions are asked on biology, chemistry, physics, earth science and math, but most of people in this field prefer dedicated mailing lists or forums such as ccp4bb, rietveld, xrayforum. $\endgroup$
    – marcin
    Oct 14, 2015 at 10:14
  • $\begingroup$ sounds good @marcin - i'll do what i can to support it! it would be great to have it all in once place. $\endgroup$
    – shigeta
    Oct 14, 2015 at 13:17

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