IF your MR solution is correct ( ie r factor falls on refinement to 40% say) and your protein A is roughly 50% of the complex, and IF your data is good to 1.9A (assumed SG correct etc) I would do my best to correct any obvious rebuilding needed for protein A, ( r factor should fall further if this is done well) , then as others suggest fit an idealised alpha helix or two, then try rebuilding again with the best sequence you can derive fir B. Once r factors in the 30-40% range you can often fit a “ val leu phe “ type sequence. I personally find this sort of challenge fun ! But maybe others don’t... Eleanor
On Sat, 4 Nov 2023 at 19:55, Randy John Read <[email protected]> wrote: > 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 <[email protected]> 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: > [email protected] > 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/ > ######################################################################## 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/
