I23 data deposition

If the structure has been refined against an I23 dataset, users can deposit the PDB and structure factors conventionally via the PDB ONeDEP System.

• Deposition guide
• Video deposition guide

On the other hand if the I23 dataset has been used for experimental phasing but not for refinement, we ask users to link the I23 dataset to their dataset used for refinement. The steps to do so are shown below. In case of any problem, do not hesitate to contact I23 staff members.

The PDB website accepts only one structure factor file per PDB file, thus the native and the I23 mmcif files should be combined. This can be done in Linux or Mac run:

cat file1.cif file2.cif > file_combined.cif.

The 1st block/dataset being the one used for your final refinement and the 2nd one, the I23 dataset. The deposited file will have two blocks, but only the 1st block will be validated, so one has to make sure that the 1st block is the one for refinement.

The mmcif can be deposited as a normal structure factor file but requires filling the I23 information at 3 different places on the PDB ONeDEP System website:

• In the 'Data collection tab', under 'Collection Source' (1), you should fill in the data collection parameters for the refined data, and then click the '+' (2) button to add another collection source, you will then be able to fill the I23 beamline parameters. The PDB website would expect wavelenght between 0.5 and 2Å, filling a longer wavelength would trigger a yellow warning message (3), but this does not affect the depostion (same goes for the sample temperature). For the detector, choose 'Dectris Pilatus 12M' (4).

• In the 'Data collection tab', under 'Software used' you can add the software related to the I23 data (if they are different from he one used for the native data, ie phasing: HKL2map).

• In the 'Data Collection tab', under 'Collection Statistics', press the (+) button to be able to add the statistics for the I23 dataset for the overall data quality and data quality in resolution shells.