That is some blob! What is the expectd ligand? It is hard to see in these pictures but are there rings? other chemical features? to be seen
You could let Arp/War build dummy atoms into it - and see what it makes. Eleanor On 4 February 2017 at 15:03, 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 > > >
