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
deposit@rcsb.rutgers.edu.
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:
fsrv1.bmc.uu.se/eds/eds_sos.html
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
(deposit@rcsb.rutgers.edu). (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 eds@xray.bmc.uu.se
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. 
|
|
