Don't forget to check the anomalous difference Fourier - this may fix any S atoms - the resolution is god enough Eleanor
On 18 January 2015 at 01:12, Robert Stroud <str...@msg.ucsf.edu> wrote: > I suspect it may be a reaction with your reducing agent. What did you use > either in the preparation, or in the crystallization. If you didn’t have > reducing agent it probably oxidized to sulfuric acid. You should figure it > out with difference maps and maybe mass spec also. > bob > > On Jan 17, 2015, at 4:10 PM, sreetama das <somon_...@yahoo.co.in> wrote: > > Hi, > Thanks for the quick replies. > I modelled in CME and refined. However, I get a blob of negative density > around the S-S bond, which is retained up to 5 sigma. > Does it mean it is not CME ? > > Thanks & regards, > sreetama > > > On Sunday, 18 January 2015 12:41 AM, Roger Rowlett <rrowl...@colgate.edu> > wrote: > > > If CSO does not account for the density -- the SO bond should be about 1.8 > A IIRC -- a possibility is an adventitious metal ion. > Roger Rowlett > On Jan 17, 2015 1:25 PM, "sreetama das" <somon_...@yahoo.co.in> wrote: > > Dear Users, > > I am solving a structure from x-ray diffraction data (1.62A resolution). > > The protein has a single cysteine residue (which is also the catalytic > residue), and it has a positive density on it (fig 1; R/Rfree = > 16.88/19.94). The positive density is retained upto 11.5 sigma level. > > Modelling with water retains the positive density (fig 2; R/Rfree = > 16.85/19.94) upto 5.2 sigma level. > > Modelling with CSO (S-hydroxycysteine, fig 3, R/Rfree = 16.82/ 19.81) > produces partial positive and negative densities, which are retained upto 5 > sigma. Moreover, after real-space refinement in coot followed by refinement > in refmac, the N-terminus of CSO is not bonded to the preceding residue, > nor is its C-terminus bonded to the succedding residue. > > All maps are contoured at 1sigma (2Fo-Fc map) and 3sigma (fo-fc map). > The protein preparation contained Tris buffer at pH 7.2, NaCl, glycerol > and beta-mercaptoethanol (2mM), while the crystallization condition > contained citric acid (pH 3.5) and ammonium sulfate. > > Please suggest how to interpret the data. > > thanking in advance, > sreetama > > > > <coot_CME.png> > > > all the best! > > Bob > > > >
