Hi Sam, What you write does not sound good to me. Did you have Phaser check "all possible [spacegroups] in same pointgroup" (this is how it is called in ccp4i)? P321 is quite rare, compared to P3121 and P3221. If you miss a screw axis, you will not find a solution. An R-factor of 50% does not at all prove that the solution is correct.
Finally, an outer-shell CC1/2 of 0.9 means that the crystals diffract significantly higher than 1.9A (maybe 1.7A or even better). You should use much more data from that data collection rather than truncating at 1.9A; even data from the corners of the detector are useful if there is diffraction recorded (with, say, I/sigma >1 or CC1/2>0.14 ). There exists no "completeness police" that would tell you "the completeness in your highest shell is less than 90% so you cannot use these data" or similar. In particular if you have little sequence knowledge for chain B, you want to maximize the information gained from the experiment; this helps the maps, the refinement, and therefore the sequence assignment. Every reflection carries some amount of information; that amount depends on how accurately it is measured. If the detector edges were limiting the max resolution and you have more crystals, collect additional datasets at closer distance. HTH, Kay On Mon, 6 Nov 2023 13:09:59 +0800, Sam Tang <samtys0...@gmail.com> 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 <kahkashantari...@gmail.com> >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, <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 > >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/
