Hi there, To my knowledge the PDB does not include unmerged data in entries - you are required to deposit the data that the coordinates were refined against.
I believe you can deposit other data which will be archived and can be requested by other users - problem is that none of the distribution web sites fesses up to the existence of these extra datasets as part of the entries - so users of your structure will be ignorant of them. You could ask for an authors' remark to be included in the appropriate part of your coordinate header to alert users to the archived material. Currently you can upload data as mtz files and this format would of course be most that would be the most convenient. Of course the mmcif format could include the deposition of unmerged data. Currently some distributed mmcif SF files in fact have multiple datasets - so for example relating to other crystals or other wavelengths. So you could simply provide your unmerged data as an mmcif block to include at the end of the dataset used for refinement. I'm guessing eds and pdbredo just pick up the first block as representative of the entry. But you can include other stuff after it. Again it would be useful to ask for explanatory remarks to be included for users of the data. For example, the authors of the excellent structure 3ne5 submitted a 'phasing dataset' with their SFs. This appears (after 'Format standardization' 2013-08-28) at the end of the native refinement dataset and I imagine refers to a SeMet crystal. (Although the values are so small I think they are perhaps the estimated intensities of just the anomalous-substructure? If you are interested, below is a bit from that file starting with the end of the native data - I imagine the negative sigmas indicate absent reflections). You can check the mmcif dictionary at http://mmcif.rcsb.org/dictionaries/mmcif_pdbx.dic/Categories/refln.html to see whether you can find an appropriate category for your data. I hope the PDB will be happy to spend the time required to negotiate with you an appropriate representation (although I was told that time constraints often mitigate against this). all the best Martyn <<snip>> 1 1 1 47 1 25 o 306.1 133.1 1034.6586 1520.8234 1 1 1 47 1 28 o 348.2 137.8 1795.0702 1421.0972 #END data_r3ne5Asf # _cell.entry_id 3ne5 _cell.length_a 160.076 _cell.length_b 160.076 _cell.length_c 680.069 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 # _diffrn.id 1 _diffrn.crystal_id 1 _diffrn.ambient_temp ? _diffrn.crystal_treatment ? _diffrn.details ' SeMet phasing set' # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97920 # _entry.id 3ne5 # _exptl_crystal.id 1 # _reflns_scale.group_code 1 # _symmetry.entry_id 3ne5 _symmetry.space_group_name_H-M 'H 3 2' # # loop_ _refln.crystal_id _refln.wavelength_id _refln.scale_group_code _refln.index_h _refln.index_k _refln.index_l _refln.status _refln.pdbx_I_plus _refln.pdbx_I_plus_sigma _refln.pdbx_I_minus _refln.pdbx_I_minus_sigma 1 1 1 1 0 -29 o 13.6 1.1 0.0 -1.0 1 1 1 1 0 -26 o 4.3 0.4 0.0 -1.0 1 1 1 1 0 -23 o 13.1 0.8 0.0 -1.0 1 1 1 1 0 -20 o 141.7 5.0 0.0 -1.0 1 1 1 1 0 -17 o 305.0 10.6 0.0 -1.0 1 1 1 2 -1 15 o 189.0 6.2 178.5 6.8 <<snip>> ________________________________ From: Raji Edayathumangalam <[email protected]> To: [email protected] Sent: Friday, 6 September 2013, 3:42 Subject: [ccp4bb] What kind of reflection data to deposit to PDB Hi Folks, Sorry for the non-ccp4 post. I am trying to determine what is the best form of unmerged reflection data to deposit to the PDB. I have single wavelength anomalous data for my structure and I have two flavors of scaled files from the same exact set of diffraction images: (1) data indexed and scaled in p1, and (2) data indexed in p222, scaled in Scalepack using the "no merge original index" option and converted to .mtz since the unit cell in the header of the output .sca file was missing. The space group for the dataset is p212121. Please could you let me know what might be the best approach. Many thanks and cheers, Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
