Take the 2-minute tour ×
Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required.

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?

share|improve this question

1 Answer 1

up vote 3 down vote accepted

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.

share|improve this answer

Your Answer

 
discard

By posting your answer, you agree to the privacy policy and terms of service.

Not the answer you're looking for? Browse other questions tagged or ask your own question.