How are the peaks coordinated? Regular coordination with 5 or more ligands has ion written all over it. Different difference density peak heights can be caused by differences in effective B-factor restraint weight but also by differences in relative scattering factors of oxygen and whatever you have.
Cheers, Robbie Sent from my Windows 10 phone Van: Keller, Jacob<mailto:kell...@janelia.hhmi.org> Verzonden: donderdag 13 april 2017 13:05 Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Onderwerp: Re: [ccp4bb] waters with positive FoFc peaks? It would be useful to know what wavelengths you were talking about. Also, try an anomalous difference Fourier map to see whether the atoms are weakly anomalous. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew Marshall Sent: Thursday, April 13, 2017 2:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] waters with positive FoFc peaks? Hello all, I have a 1.8A structure (Rfree/Rwork = 20.5/17.4) with 1420 water molecules modelled. There are approximately a dozen waters, all well structured with hydrogen bonds to protein atoms, with positive difference density (>4sigma, sometimes >5) at their centre. The only ions present in my buffer were Cs, Cl and a small amount of Na. I thought Cl ions might be a possibility, but many of them are in close proximity to acidic residues and/or one-another. It's probably worth noting that the same structure solved using data to 2.25A from the same crystal at a different wavelength doesn't contain these peaks (the offending waters look normal). Has any come across this before? Thoughts? Thanks, Andrew Marshall PhD Candidate Laboratory of Protein Crystallography Dept. of Molecular and Cellular Biology School of Biological Sciences The University of Adelaide
