Re: [phenixbb] sequence independent model building possible?
To check if you crystallized a contaminant, use https://strube.cbrc.kaust.edu.sa/contaminer/ HTH, Kay
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
On 02/05/2016 01:01 AM, Kaushik Hatti wrote: 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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Dear all, I am solving a structure at 1.28 Å. On the ligand, there are some patches of negative electron density till 3.5 RMSD. It will be highly appreciated if someone can tell the maximum RMSD of allowed negative electron density in structure. Thank you! With regards, Bishal Singh PhD student German cancer research center (DKFZ) University of Heidelberg, Germany
Dear all, I am solving a structure at 2.28 Å with an ice ring around 3.3 Å. In this ice ring region, the completeness of data is reduced to 72%. Is this normal for the ice rings? Another question is that, when I do real space refinement the RMS deviation with Rwork/Rfree are increasing. Is it a good idea to ignore real space refinement if the all residues are fitting well in electron density? Your reply will be highly appreciated. Thanks a lot! With regards, Bishal Singh PhD student German cancer research center (DKFZ) University of Heidelberg, Germany
Hi Bishal, yes I guess it's fine to do so. Pavel On 2/7/16 01:16, Singh, Bishal wrote:
Dear all, I am solving a structure at 2.28 Å with an ice ring around 3.3 Å.
In this ice ring region, the completeness of data is reduced to 72%. Is this normal for the ice rings?
Another question is that, when I do real space refinement the RMS deviation with Rwork/Rfree are increasing. Is it a good idea to ignore real space refinement if the all residues are fitting well in electron density?
Your reply will be highly appreciated. Thanks a lot!
With regards, Bishal Singh PhD student German cancer research center (DKFZ) University of Heidelberg, Germany
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Hi, above 3 "sigma" is alarming. Possibilities are: - it is misplaced; - parameters are not refined well (till convergence, for example); - it is partially occupied so you need to refine occupancy (one q per entire ligand). Pavel On 2/7/16 00:42, Singh, Bishal wrote:
Dear all, I am solving a structure at 1.28 Å. On the ligand, there are some patches of negative electron density till 3.5 RMSD. It will be highly appreciated if someone can tell the maximum RMSD of allowed negative electron density in structure. Thank you!
With regards, Bishal Singh PhD student German cancer research center (DKFZ) University of Heidelberg, Germany
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participants (3)
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Kay Diederichs -
Pavel Afonine -
Singh, Bishal