Hi,
If I remember correctly this angle is for the planarity of the peptide bond.
Maybe you have a real deviation which might occur not so seldom than expected.
You have a quite high resolution. If the density is really convincing then you
may accept this outlier. Not every outlier is a mistake. However with 2.55°
the r.m.s.d. for your angles is quite high I think.
Christian
Am Donnerstag 16 Februar 2012 18:00:10 schrieb Greg Costakes:
> Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees
> (not bond length). MolProbity states that my only abnormal angle is 124.23
> degrees between O--C--N of an Arg. Real Space Refinement does not change
> anything and Regularizing the zone completely distorts the backbone. Any
> suggestions on how to fix this?
>
> ---------------------------------------------------------------------------
> ---- Greg Costakes
> PhD Candidate
> Department of Structural Biology
> Purdue University
> Hockmeyer Hall, Room 320
> 240 S. Martin Jischke Drive, West Lafayette, IN 47907
>
> ---------------------------------------------------------------------------
> -----
>
>
> ----- Original Message -----
> From: "Bernard D. Santarsiero" <[log in to unmask]>
> To: "Greg Costakes" <[log in to unmask]>
> Sent: Thursday, February 16, 2012 11:42:55 AM
> Subject: Re: [ccp4bb] Bond Length Outliers
>
> Greg,
>
> Your RMSD on bond lengths should be around 0.01A (your structure vs.
> idealized library), and the RMSD on bond angles should be around 1.5deg.
> You must be using an incorrect value of the weight factor between
> structure factors and geometric factors, and relying too heavily on
> structure factors.
>
> Bernie
>
> On Thu, February 16, 2012 10:31 am, Greg Costakes wrote:
> > I am currently in the final steps of refining a 1.3A structure and am
> > coming across a slight problem. According the the pdb file, I have an
> > Rmsd bond length of 2.55. MolProbity identifies three outliers which
> > correspond to the bond lengths of:
> > Asp: C--O , bond length = 1.2A
> > Arg: C--O , bond length = 1.15A
> > Ala: N--Ca , bond length = 1.43A
> >
> >
> > Real space refinement in Coot does not help and if I Regularize the zone
> > it completely distorts the backbone. So my question is, how do I fix
> > these bond length outliers? Do I need to be concerned with them? Any
> > advice will be much appreciated. Thank you!
> >
> >
> >
> > -------------------------------------------------------------------------
> >------ Greg Costakes
> > PhD Candidate
> > Department of Structural Biology
> > Purdue University
> > Hockmeyer Hall, Room 320
> > 240 S. Martin Jischke Drive, West Lafayette, IN 47907
> >
> > -------------------------------------------------------------------------
> >-------
>
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