Dear all Thanks again for more input to the question. And credits to Eleanor and Kay for pointing out the high R-factor and possible issue with the space group. Their advice prompted me to revisit the MR solution and it happens that another solution, in P3121, gave a better map with R-factor after one round of refinement being 0.33/0.36, which was a remarkable difference with the P321 solution (R~0.5).
So the next step I would take would be to re-try Arp/warp and see if things work out with poly-A. I shall update the community with the outcome. Kind regards Sam On Tue, 7 Nov 2023 at 01:13, Rafael Marques <rafael_mmsi...@hotmail.com> wrote: > Hi Sam. > > > > If you still have any of your crystals or any protein solution left in the > well you harvested your crystals, I would run a MS/MS with them. Next step > would be to run AF with your known chain A and your best Mass Spec hit (s), > and use the resulting model for MR. > > > > Good luck > > > > > Rafael Marques da Silva > > PhD Student – Structural Biology > > University of Leicester > > > > Mestre em Física Biomolecular > > Universidade de São Paulo > > > > Bacharel em Ciências Biológicas > > Universidade Federal de São Carlos > > > > phone: +55 16 99766-0021 > > > > * "A sorte acompanha uma mente bem treinada"* > > *________________________________________________* > > > ------------------------------ > *De:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> em nome de Boaz Shaanan > <bshaa...@bgu.ac.il> > *Enviado:* Monday, November 6, 2023 2:41:43 PM > *Para:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Assunto:* Re: [ccp4bb] About model building > > Hi, > If you still have crystals left, you could soak crystals with KI3 and > collect data at Cu wavelength for SAD phasing, which could help you to > resolve the missing piece. Maybe. > Cheers, > Boaz > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben Gurion University > Beer Sheva, Israel > > On Nov 4, 2023 10:04, 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 > > ------------------------------ > > 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 > ######################################################################## 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/
