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 <[log in to unmask]> 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 RowlettOn Jan 17, 2015 1:25 PM, "sreetama das" <[log in to unmask]> 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
