Dear Wei, I am not sure which molecule this density corresponds to but I think you should also consider the possibility of a molecule that can be fitted in the density but is in fact at a special position meaning that the axis of symmetry passes through the center of the molecule leading to presence symmetry related molecule also in the same position. However, this would obviously mean that the atoms of these two molecules would have partial occupancies.
Best, Tushar. On Mon, Nov 28, 2016 at 5:27 PM, Bythell-Douglas, Rohan R < r.bythell-doug...@imperial.ac.uk> wrote: > Dear Wei, > > I think Prem’s suggestion that the molecule is on a symmetry axis is > right. There are 2 images in those that you have sent that show a two fold > rotation axis within the missing density, so I think the density > corresponds to two molecules. - possibly something like PMSF? Did you > happen to use PMSF during your purification? > > Regards, > Rohan > > On 28 Nov 2016, at 11:36, Prem Prakash <prem...@gmail.com> wrote: > > Dear Wei, > I am not sure but is it possible that the crystallization condition you > have used has already this compound (may be as an impurity) rather than > expecting this as an extract from E. coli. If that can be searched it may > be useful. > > Good luck > Have a nice day > > On Mon, Nov 28, 2016 at 3:51 PM, LiuWei <we...@icloud.com> wrote: > >> Hi Prem, >> >> Thanks for your response. The compound really looks to be a two-fold >> symmetry related molecule, but I am very sure that it is not located at a >> symmetry axis. It looks like a compound with 3 or 4 terminal ring, could-be >> two molecules of biphenyl enter. Such a compound, however, is almost >> insoluble, and I wonder if it can be copurified with a protein. >> >> Regards >> Wei >> >> 2016年11月28日 下午02:50，Prem Prakash <prem...@gmail.com> 写道： >> >> Hi Wei, >> Is the electron density of this compound lie at the symmetry axis ? It >> seems to me that two planar rings with one connecting oxygen. And the >> compound is more looks like a diphenyl ether to me with its symmetry >> related molecule. >> >> Hope others will give some more idea about it. >> >> Cheers >> P.P >> >> On Sun, Nov 27, 2016 at 4:03 PM, Wei Liu <we...@me.com> wrote: >> >>> Dear all, >>> >>> We have recently crystallized a recombinant protein produce from E. >>> coli, and determined the structure at 1.9 Å. The asymmetric unit contains >>> two protein monomers. Beyond our expectation, strong Fo - Fc density is >>> present at a cleft of one subunit, but not in the other. Density maps are >>> given in the snapshots attached to this email. We tried to model Tris or >>> Bis-tris propane that were used as the purification and crystallization >>> buffers, but apparently either of them poorly fitted in this density. The >>> molecule that can be modeled here seems more likely to be a ligand >>> comprising 3 or 4 rings with good planarity, however we did not add any >>> additives in our crystallization trials. So we think it should be something >>> from E. coli, which has high affinity to our protein. I wonder if anybody >>> can figure out which molecule well fits to the electron density. >>> >>> Best wishes >>> Wei Liu >>> >>> >>> <Snapshot1.png><Snapshot2.png><Snapshot3.png><Snapshot6.png> >>> <Snapshot4.png><Snapshot5.png> >>> >> >> > > Rohan Bythell-Douglas > rbyth...@ic.ac.uk > Section of Structural Biology, > Dept. Medicine, > Imperial College > London SW7 2AZ > > > > -- Tushar B. Raskar Project JRF (DBT), Protein Crystallography Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology - Bombay.
