The validation reports are pretty bad, so it seems to be a case where the referees and editor have not checked them. And, like Herman wrote, the models do not appear to agree well enough with the maps - in all three cases.
Mark J van Raaij Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 > On 19 Jul 2019, at 15:46, herman.schreu...@sanofi.com wrote: > > 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 > <mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag von Rhys Grinter > Gesendet: Freitag, 19. Juli 2019 15:22 > An: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > Betreff: [EXTERNAL] [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2 > > EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk > <mailto: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 > <https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
