DATA DEPOSITION AND PROCESSING

Restarting ADIT Depositions

A structure can be deposited in more than one Internet session by using ADIT's "Session Restart ID" feature. This identifier appears in red in the center of the browser window when ADIT's "deposit" step is first started. It is also seen in the title of the browser throughout the deposition session.

The case-sensitive restart ID should be entered in the space provided on the ADIT home page to return to the undeposited entry. Any data entered in a category are stored every time the user selects the SAVE button. All entered data associated with a particular entry can be accessed using the restart ID until the "DEPOSIT NOW" button is selected, for up to six months after the session has been last updated.

ADIT is available at the RCSB PDB and PDBj. ADIT-NMR can be used to deposit data to the PDB and BMRB at the same time.

ADIT tutorials (in English and Japanese) and example "in progress" deposition sessions are accessible from deposit.pdb.org.



The ADIT Session Restart ID



Depositing and Releasing Experimental Data

The RCSB PDB strongly encourages depositors to follow the guidelines regarding the submission and release of coordinate and experimental data that have been set by the International Union of Crystallography, the National Institutes of Health, and the journals.

Deposition of experimental data (structure factor and/or NMR constraint files) is required by many journals, including Acta Crystallographica, Biochemistry, Cell, Nature, and Science.

These files can be uploaded during the ADIT deposition process.

Depending upon the hold status selected by the depositor, data release can occur when a depositor gives approval (REL), the hold date has expired (HOLD), or the journal article has been published (HPUB). There is a one-year limit on the length of a hold period, including HPUBs. If the citation for a structure is not published within the one-year period, depositors will be given the option to either release or withdraw the deposition.

Detailed deposition and release information is available from http://deposit.pdb.org.

Questions about ADIT may be sent to deposit@deposit.rcsb.org.



Weekly Deadlines for Release/Modify Entry Requests

PDB entries are processed by three members of the wwPDB (RCSB PDB, MSD-EBI, and PDBj) and are released immediately (REL), when the corresponding paper is published (HPUB), or on a particular date (HOLD).

Each week, all files scheduled for release or modification are checked and validated one final time. Authors may be contacted to resolve any issues that may arise while preparing the entries for release.

When the release of HPUB structures is requested, the wwPDB routinely confirms the primary citation. If this is not accomplished within that release cycle, the entry may be scheduled to be released in a later update.

To be included in the next weekly update, any required author correspondence should be sent to the appropriate wwPDB member by the following times:

All entries due for release are transferred to the RCSB PDB for final packaging into the master PDB ftp archive. These files are then released by 4:00 EST each Wednesday.

Requests received after these cutoff times will be processed during the next update cycle.



2007 (Jan - Mar) Deposition Statistics

In the first quarter of 2007, 2319 experimentally-determined structures were deposited to the PDB archive. Of these structures, 62.7% were deposited with a release status of HPUB, 22.3% with a release status of HOLD, and 15.0% were released as soon as annotation of the entry was complete.

80.8% of these entries were determined by X-ray crystallographic methods; 18.8% were determined by NMR methods. 80.3% of these depositions were deposited with experimental data.

92.8% of the crystal structures were deposited with structure factors; 27.7% of NMR structures were deposited with restraints.