Dear Charlie Nichols, when optimizing your SHELX runs, SHELIXIR may help you in some cases (https://kmlinux.fjfi.cvut.cz/~kolenpe1/shelixir). A couple of days ago, I created quick and dirty tutorial to SHELIXIR command line: https://www.youtube.com/watch?v=dqi5_yLhWOc and also the same quality tutorial to the GUI: https://youtu.be/CZIziPv28hA There may be some parameters to further optimize in which SHELIXIR may help you (trying more space groups, optimizing of high or low resolution cut-off, solvent content). However, SHELX C/D/E is generally known to have problems at lower resolution (say 3.5 AA and lower). To say a bit more about your problem, would you share the files off the list? Btw, the great thing about SHELX is that you do not even need to know the content of the AU in some cases! Best regards, Petr ________________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Nichols, Charlie <charles.nich...@crl.com> Sent: Friday, May 6, 2022 1:17:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Phasing a difficult RNA heteroduplex structure
Dear all, I am trying to solve the structure of an RNA heteroduplex + ligand with approximate MW of 6800. * Structure likely to have a core helical region and a couple of bases of single stranded material at both ends on both strands I have datasets from visually similar crystals with different, but related unit cells: Form1: 32.70 32.70 54.55 90.00 90.00 120.00 – best native ~2.9A - different pipelines reported P62 2 2, P62 and P32 from auto-indexing - P6222 impossible to fit 1 complete heteroduplex - P62, most consistent indexing choice, 37% solvent, low Matthews probability but possible to fit 1 heteroduplex However, Xia/Dials report tNCS * If the ASU only has room for 1 copy the heteroduplex there can’t be tNCS, does this therefore mean we must have twinning? * There is a reasonable similarity NMR structure in the PDB, this is ~45A long * I am therefore guessing that the duplexes are most probably making end-end contacts to form long fibres that are ~aligned along the Z-axis and that the crystal either contains fibres bound both ways up, or that the duplex can bind either way up to create the fibres, the twinning then superposes the two orientations to create two identical repeats mimicking tNCS – does this seem a reasonable interpretation? I have a dataset with Zn/Mg exchange and good anomalous signal to ~3.8A, ShelX finds good sites but DM / phase-extension with the 2.9A native data creates a mess and there is little difference between the two hands – can you give any advice on how I might try to proceed with experimental phasing in this case? Form2: 62.40 62.40 54.82 90.00 90.00 120.00 – best native ~2.5A - Auto-indexes as P62 / P64, higher resolution data than Form1 - Again, Xia/Dials report tNCS - Cell has a doubling of a/b dimensions but c is the same - Molecular replacement fails completely - Cobalt-hexammine soak gave strong anomalous signal but only to ~6A, again ShelX finds good sites, but DM / phase-extension gives a mess - From the pathology of Form1, I am concerned that we have exactly the same issue with overlaid flipped orientations along the Z-axis Any advice on how to proceed would be greatly appreciated. Thanks, take care, Dr Charlie Nichols Charles River Laboratories ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
