Btw, re other sources of deviation: Molprobity does not report geometry deviations beyond CB. The RUN500 command from CCP4i does. BR
-----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Dale Tronrud Sent: Thursday, February 16, 2012 10:56 AM To: [email protected] Subject: Re: [ccp4bb] Bond Length Outliers (correction) Using the Protein Geometry Database (pgd.science.oregonstate.edu) I looked up all Arg residues in models with resolution of 1.3 A or better and found 5920 examples. The mean value of the O-C-N angle (and I'm assuming that the O and C atoms are in the Arg) is 122.6 deg with a sigma of 1.1 deg. 338 of them have a value greater than 124.23 deg, or about 6%. It doesn't look to me that this piece of structure is an outlier. Regularizing may move atoms out of density but it shouldn't "distort" anything, it should make it, <cough>, more regular. If regularizing is doing something bad there is a problem with the regularizer not the structure. Does you model have any ligands that might have horrible angles but not be reported by MolProbity? Dale Tronrud On 02/16/12 09:00, Greg Costakes wrote: > 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 > > ---------------------------------------------------------------------- > ---------- > > > ---------------------------------------------------------------------- > -- > *From: *"Bernard D. Santarsiero" <[email protected]> > *To: *"Greg Costakes" <[email protected]> > *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 >> >> > ---------------------------------------------------------------------- > ---------- >> >> >> > > > >
