I have seen similar features fairly often when the data collection has been pushed to the limit. The theory is that it is due to radiation damage - you could check by only merging say the first 50% of your data, then seeing if the di-sulphide is intact in those maps. ( wouldnt re-refine much - just set CB-SG occs to 0.00 - recalculate SFs and check the maps) Eleanor
On 2 June 2014 07:44, Marjolein Thunnissen < marjolein.thunnis...@biochemistry.lu.se> wrote: > Hi, > > I would guess radiation damage, see Weik et al., 2000, PNAS 97, 623-628 > or for a more recent discussion and thorough overview Sutton et al., 2013, > Acta Cryst D69, 2381-2394. > > best regards > > Marjolein > > > On 02 Jun 2014, at 07:08, Eze Chivi <ezech...@outlook.com.ar> wrote: > > Hello, when I refine my structure, I see negative density around the > disulfide bond. I have 7 copies per ASU, and I can see this density in many > of them. In some cases, I see positive density also (negative in the center > of the straight line linking S atoms, and positive in both sides). What can > I try to solve it? Is it due to radiation damage? Alternative conformation > (partial oxidation)? Incorrect disulfide geometry parameters? My resolution > is 2.1 A, R/Rfree are around 0.220/0.243, and similar results with refmac5, > phenix and PDBREDO. Please find two example pictures in attachment. > Thanks for your help! > > > Ezequiel > <disulfide.jpg><disulfide2.jpg> > > > > > > > *Marjolein Thunnissen* > Science Coordinator MX > > MAX IV Laboratory > Lund University > P.O. Box 118, SE-221 00 Lund, Sweden > Visiting address: Ole Römers väg 1, 223 63 Lund > Telephone: +46 766 32 04 17 > www.maxlab.lu.se > >
