[phenixbb] sequence independent model building possible?

Kay Diederichs kay.diederichs at uni-konstanz.de
Sat Feb 6 08:17:45 PST 2016

To check if you crystallized a contaminant, use

>On 02/05/2016 01:01 AM, Kaushik Hatti wrote:
>> Hello,
>> Is abinitio model building possible for a map with poly alanine model
>at 1.9A resolution?
>> We thought we had crystallised our protein of interest X, collected
>data at 1.9 A and all attempts to solve protein X (which has many
>homologs) through MR failed.  All attempts to re-crystallise the same
>protein also failed.
>> Now, we think the initial protein which got crystallised could be a
>contaminant (we don't have any crystals left from this batch to check
>for the sequence of the crystallised protein).  Through various methods
>(and a bit of luck) we have arrived at a decent map with LLG : 3600 and
>TFZ: 22 and R/Rfree : 37/41 (for a poly alanine model).
>> I believe these scores indicate right fold.  As I still don't know
>the sequence information, is it possible to build sidechains directly
>from the map (I could only identify a couple of residues and the model
>largely remains PolyAla)?  Autobuild with Rebuild-in-place didn't help
>in identifying any more residues.
>> I have also searched PDB database for similar structures. But, none
>of those are either from our expression system (E. coli) or organism of
>our protein of interest. Neither did I find any similar sequences from
>E. coli or our organism of interest.
>> Any leads/suggestions would be helpful.
>> Thanks,
>> Kaushik,
>> MRN Murthy lab,
>> MBU,
>> IISc, India
>> --
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