Hello Marco, First: compare your unit cell parameters with RCSB (there is an option for that in the search, very helpful). Give it say 5% error margin.
Worst case scenario - cry a little, having found that your protein is something else... Next, check in depth for space group oddities, twinning, or general data misbehavior. Next, split your helicase into two lobes (if this is the right kind of helicase) and do MR with both halves, like it was a complex of two proteins (requires a bit of skill with MR - but nothing terrifyingly hard tbh). If there are more domains - split into more (RQC, HRDC, etc.) Hope this helps. Artem On Mon, Feb 19, 2024, 5:54 PM Marco Bravo <[email protected]> wrote: > Hello all, > I recently collected data on some plate crystals for a previously > uncharacterized protein at the ALS light source. The XDS auto-data > processing log output indicates that my resolution is 2.8 angstroms. The > protein is a helicase with homologs already in the protein data bank making > it a suitable target for molecular replacement which I thought initially. > However after trying molecular replacements with all known homologs in the > protein data bank the R values remain high after MR >0.5. After an initial > round of Rigid body or restrained refinement. The R values still remain > very high at around >.5. I have tried MR with Rosetta and alphaphold models > but the problem of high R values persists. The best solution I get is from > the CCP4 cloud automatic molecular replacement and model building pipeline > which gives me a free R value of 0.46.. However the solution is only for > residues ~100-326 out of a 543 amino acid long protein. And even then the > model still has a lot of missing residues and truncated sidechains and > overall fits the map quite poorly. Does anyone have any suggestions about > how I can solve my structure if at all possible at this point? I ran the > crystals and pre-crystalized samples on a gel and it appears that the > protein remains stable during crystallization as the molecular weight did > not change or any degradation does not appear. > > ######################################################################## > > 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/
