Correction! I mean't 6BV0 et. al. Many apologies!!! Thanks Paul Brear for pointing this out.
Rhys On Wed, 24 Jul 2019 at 21:36, Rhys Grinter <rhys.grin...@monash.edu> wrote: > Hi All, > > Thanks for all the helpful comments and discussion surrounding my last > post. I've been doing a little more investigation into this issue and > wanted to see if people were able to provide me with some additional > opinions/insights. > > I investigated the PDB entries for the lead deposition author of the > 6MO0-1-2 series: Lin, Y.-L. ( > http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=50E454B). > With some slightly alarming results. > > A number of additional entries appear to have ligands associated with > questionable density.: > > 6VB0,1,2,3,4 and 6BUY – Density does not support amino acids modelled and > there are questionable interactions with protein and solvent (Published > Scientific Reports 2017) > > 4NZ8, 4NAQ – Questionable density for peptide modelled, bad/unrealistic > interactions with protein (Published PNAS 2012) > > 4HOM – Questionable density for peptide modelled. Fo-Fc map density on > refinement seems more interconnected than would be indicated by water, > however density does not fit peptide modelled. Bad/unrealistic interactions > with protein observed, specifically Phe7 of peptide (chain B) (Published > PNAS 2012, same paper as 5NZ8 and 4NAQ) > > 4KXD et. al. – Questionable density for amino acids in both EDS maps and > re-refined with SF and model minus ligand. Poor R-factors obtained for 4KXD > on refinement (W 0.27,F 0.33) (Published JBC 2013) > > These constitute many of entries associated with this author (some other > not mentioned appear are okay) and it makes it seem much less likely to me > that modelling of the structures from my previous post are a result of lack > of experience or poor supervision. > > It is in my opinion a huge problem for the field and science in general, > if structures like this are making it into publications in well respected > journals. > > Best Wishes, > > Rhys > > -- > Dr Rhys Grinter > NHMRC Postdoctoral Researcher > Monash University > +61 (0)3 9902 9213 > +61 (0)403 896 767 > -- 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
