Hello Marco, This may seem a little obvious, but did you check the sequence of your protein from the gel/ crystals? I've found mass spec to be very useful in this regard as we've had at least two instances of having a protein that looked to be the right size/ correct protein, but wasn't after mass spec analysis. Good luck, tom ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Marco Bravo <mbrav...@ucr.edu> Sent: Tuesday, February 20, 2024 9:44 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Difficult Molecular replacement
[You don't often get email from mbrav...@ucr.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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/
