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 > <mailto: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
