If you "multi-chicken" your 2fo-fc map in coot... (Extensions > maps > multi-chicken)
... You might be able to pick out where different atoms are by comparing the peak height with the near-by protein atoms (ADPs & occupancy notwithstanding). At your resolution you will be able to see that O > N > C and anything bigger like P or S atoms will appear enormous. Maybe the nature of the enzyme will help you out here? Does it have a known substrate or co-factor that might have been pulled through purification? HTH, Dave On Sat, 4 Feb 2017, 21:24 Kevin Jin, <[email protected]> wrote: > According to your first fig. The Ser may carry a dual conformation. If > then, the occ ration could be ~ 7:3 > > According to your 1st, 2nd and 3rd figures, the geometry of the density > is tetrahedral. Can it be PO4 with the same occ (~70%) ? > > If there were more figures available, the geometry of the unknown density > could be more clear. > > Can You try Glucose phosphate withe occ of 70%? > > On Sat, Feb 4, 2017 at 7:03 AM, sharifah nur hidayah syed mazlan < > [email protected]> wrote: > > Dear All, > > I am working on a structure with an unknown blob extended from the gamma O > of the catalytic serine residue. The resolution of the dataset is 1.38 A. I > have no idea whether the residue is modified or the blob belongs to other > molecule. > > The protein was expressed in Rosettagami (DE3), purified using > Ni-Sepharose (affinity chromatography) and Q-Sepharose (Anion exchange > chromatography). The crystallization formulation used contain 15% PEG 8000, > 0.2 M Ammonium sulphate, 0.1 M sodium cacodylate trihydrate pH 6.5; and the > buffer composed of 50 mM Sodium chloride and Phosphate buffer pH 8. No > protease inhibitor was used (eg: PMSF) > > I have tried to fit in diethylene glycol as shown in one of the attached > figures, but as observed, it is not really fit and the molecule is in > incorrect conformation. > > Kindly help me with this matter. > > > > Thanks and regards, > > Sharifah Nur Hidayah > Universiti Putra Malaysia, > Malaysia > > > > > > -- > Kevin Jin > > Sharing knowledge each other is always very joyful...... > > Website: http://www.jinkai.org/ > > -- [image: --] David Briggs PhD [image: https://]about.me/david_briggs <https://about.me/david_briggs?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links>
