Submission of Structure Factor Data to the PDB
In a recent message to the PDB list server Gerard Kleywegt and Alwyn Jones have requested crystallographers worldwide to deposit structure factor data for existing and future PDB entries. The PDB strongly supports this request.
PDB tries to make the submission of structure factor data as easy as possible. Data can be submitted in any format with an accompanying description of content. Structure factor data for new entries can be uploaded along with coordinate data at the time of deposition. For existing entries depositors can simply mail structure factor data to firstname.lastname@example.org.
As emphasized in the following message, the structure factor data are an important component of the PDB archive. We ask for the cooperation of all crystallographers to help strengthen the scientific content of the PDB archive by depositing structure factor data for all of their entries both new and old.
Dear colleague !
At present, structure factor data are available for only about *half* of all crystal structures in the PDB. Unless we all make a serious effort now, we must fear that these data will be lost to science for all eternity. Therefore, we would like to encourage all macromolecular crystallographers to check if any of their PDB entries perhaps do not have the associated structure factors deposited. To help you do this, a simple form to query the RCSB database is available at this URL:
Simply type (a unique part of) your name and hit the "Check" button to get a list of any and all such entries. If there are any, please try and track down the structure factors (on old disks, tapes, or by asking former students and post-docs, etc.) before they are lost forever. If you find any, please send them to the RCSB (email@example.com). (By the way: the most likely future user of deposited structure factor data are you yourself !!)
As you may know, we have been working on creating an archive of electron density maps for all crystal structures in the PDB for which structure factor data have been deposited - the Uppsala Electron Density Server (EDS; URL: fsrv1.bmc.uu.se/eds). At present, in about one percent of cases, we are unable to calculate a map at all, and for another ~15% of cases we are unable to reproduce the published R-value to within five percentage-points. The webpage with the search form mentioned above also contains a request for you to help us improve our ~85% success rate with EDS map calculations.
These two initiatives combined will help to preserve and improve the wealth of macromolecular crystallographic data in the public databanks and to make them available and easily accessible to the entire scientific community (cell and molecular biologists, medicinal chemists, crystallographers, etc. etc.) now and in the future.
Thank you for your time and help in advance !!
--Gerard Kleywegt & Alwyn Jones
P.S.: please direct technical correspondence about EDS to firstname.lastname@example.org
P.P.S.: in this request it has been tacitly assumed that coordinates of all published structures have been deposited already. In cases where this is not so, you are of course also strongly encouraged to dig up the models and deposit them together with the corresponding structure factors.
P.P.P.S.: please help this initiative by bringing it to the attention of colleagues who may not read the electronic crystallographic bulletin boards.