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" <b...@uic.edu> > To: "Greg Costakes" <gcost...@purdue.edu> > 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 > > > > ------------------------------------------------------------------------- > >------- >
