Hi Rhys, There is definitively some density present for a ligand, but the active site region looks completely misfitted, and the ligand density may also belong to unfitted protein residues. One first needs to get the protein chain right, and should then look if there would still be density available to fit the ligand.
Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Rhys Grinter Gesendet: Freitag, 19. Juli 2019 15:22 An: CCP4BB@JISCMAIL.AC.UK Betreff: [EXTERNAL] [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk Hi All, I was chatting with a colleague during a recent synchrotron visit and they'd recently come across some ligand/drug bound structures associated with a paper recently published in a high impact factor journal. They had pulled the associated SFs from the PDB and found that the electron density associated with these ligands didn't match that reported in the paper and certainly wasn't sufficient to model the alleged ligand. I also pulled the structure factors and after refinement in the presence/absence of the alleged ligand I also feel that the density present does not warrant modelling of the ligand. I was hoping that the community might be able to give me an outside opinion on these datasets (PDB IDs: 6MO0, 6MO1, 6MO2) and if the problem associated with the data is verified, provide some advice on how to proceed. This isn't the first occasion I've seen ligand bound structures with questionable density deposited in association with papers in well respected journals. Despite improvements to validation I feel that this problem is widespread. Best Regards, Rhys -- Dr Rhys Grinter NHMRC Postdoctoral Researcher Monash University +61 (0)3 9902 9213 +61 (0)403 896 767 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=KR65gleAznAqJKiHPp9vvVZeSsv8LHvr5PDyckgEaWw&s=NmR2g-LBQtuhDFsFRJPffbzIm3cQQWMhK7ozfrse7KY&e=> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
