You may as well have fun by manually building your molecule B into 1.9A ed map when R-factors are already in mid 30s.
Vaheh From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Sam Tang Sent: Monday, November 6, 2023 2:02 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] RES: [ccp4bb] About model building 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<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>> em nome de Boaz Shaanan <bshaa...@bgu.ac.il<mailto:bshaa...@bgu.ac.il>> Enviado: Monday, November 6, 2023 2:41:43 PM Para: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto: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<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<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<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<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/