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:[log in to unmask]] On Behalf Of Dale Tronrud
Sent: Thursday, February 16, 2012 10:56 AM
To: [log in to unmask]
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" <[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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