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 < shn.hida...@gmail.com> 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/
