Dear all Thanks for all the input. I will definitely try out in the coming couple of days. To provide more information: - the data was checked in Xtriage and no major pathology was found. Completeness was 99.2% with multiplicity of >13. Mean I/sigma(I) 18.8, CC1/2 for outer shell 0.902. - After one round of refinement, the R-factor was around 0.5, which looked reasonable given the incorrect B-chain was not removed and sequence deviations in chain A not yet rectified. - While I said Arp/warp failed to rebuild the model, it did return 3 helices in chain A and one in chain B when I ran in the QuickFold mode (secondary structure tracing) later on. So I am going to start with the helix in chain B and see how further manual rebuild goes.
Thanks again and I shall send an update for any progress. Kind regards Sam On Sun, 5 Nov 2023 at 06:26, Firdous Tarique <[email protected]> wrote: > Do the mass spec of your crystal to identify the other protein. Once done > solve your structure and build the complete model. This should be straight > forward and quick. > > Best Wishes > > On Sat, 4 Nov 2023, 09:05 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 >> > ######################################################################## 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/
