Dear Pavel,
Is this density located on a symmetry axis?
There is quite often a lot of "noise" around these regions - and it may not, in fact, be possible to model this satisfactorily.
Tony.
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Dr Antony W Oliver
Senior Research Fellow
CR-UK DNA Repair Enzymes Group
Genome Damage and Stability Centre
Science Park Road
University of Sussex
Falmer, Brighton, BN1 9RQ
email: [log in to unmask]
tel (office): +44 (0)1273 678349
tel (lab): +44 (0)1273 677512
On Feb 25, 2013, at 10:03 AM, Natashin Pavel wrote:
> Hello everyone,
>
>
> I’m working on a structure with a 1.72Å resolution data and almost finished it. But there is a piece of unknown density between two protein molecules.
> The following pictures show this density from two sides:
>
> http://www.4sync.com/photo/WHewU7Ek/Density_1.html
>
>
> http://www.4sync.com/photo/RM3IEesw/Density_-_2.html
>
> This density is located between two protein molecules and is not connected to either of them.
>
> I have tried to fit several small organic molecules from crystallization conditions and protein sample buffer, also tried ligand database search using “Phenix ligand identification” software, but no satisfactory results.
> Crystallization condition: DL-Malic acid
>
> Sample Buffer: Bis-Tris, EDTA
>
> Reagents from protein purification step (also checked): Tris, Urea, Triton-X100, DTT.
>
>
>
> I will very much appreciate to hear any suggestions and ideas on what to do.
>
> Best regerds,
>
> Pavel V. Natashin
>
>
> PhD student
> Photobiology Laboratory
> Institute of Biophysics
> Russian Academy of Sciences Siberian Branch
> Krasnoyarsk 660036, Russia
>
> National Laboratory of Biomacromolecules
> Institute of Biophysics Chinese Academy of Sciences
> Beijing 100101, China
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