Hmmm - r 50% rather suspect.. do the MR solutions from phaser and molten agree? Eleanor
On Mon, 6 Nov 2023 at 05:10, Sam Tang <[email protected]> wrote: > 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 > ######################################################################## 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/
