Hi, At 1.9A resolution there should be lots of possibilities, depending on the details.
You imply you have partial sequence information for chain B. Is there a genome for your plant or a relative of it? You could search for possible matches to your sequence, and then test all the AlphaFold models for the sequences that come up. When you say chain A has known homologues, what was the sequence identity of the homologue you used as a model? If it wasn’t pretty high, you may well be better off using an AlphaFold model of the correct sequence for A. Do you expect chain B to have helices or do you see helices in the map? Just adding some poly-Ala helices (which will tend to be locally very accurate if incomplete) will help to improve your phases. Arcimboldo would be a good tool for this, and you should also try it for completing from chain A. Do you have any anomalous scattering signal in your data? Even if it’s not enough to solve the structure, any signal can be exploited, using MR-SAD, to improve your phases and in particular reduce model bias in your map. Of course, other people have pointed out that you should make sure you can be confident in the MR solution. Also, you didn’t mentione whether there might be any issues in the data, like twinning. Presumably you would have mentioned if there was more than one copy of each protein in the a.u. Best wishes, Randy Read > On 4 Nov 2023, at 14:04, Sam Tang <samtys0...@gmail.com> wrote: > > Dear community, > > I am solving the structure of a complex between proteins A and B, where A is > a protein with known homologs and B is a novel protein isolated from plant. > The diffraction data was at 1.9 Ang collected in-house, indexed to P321. > Using A as the search model, we have got a reasonable solution where, after > one round of refinement, the A chain fits the map pretty well. What's left > was to extend the termini and fit a few rotamers. > > For protein B (B chain) I have tried the web version of ARP/wARP but the > outcome was not really good. The model was not successfully built as > indicated by low model completeness and score. The tricky thing may be that > we do not have the complete sequence information of this protein B in-hand. > (The other way round, we more or less wish to rely on the high resolution > data to confirm its sequence.) What approach would you then recommend to > build the B chain in this scenario? > > Thanks in advance and best regards, > > Sam > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## 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/
