[phenixbb] DNA covalent bond angles deviate from PDB standard dictionary

[Paul Adams]

Hi Scott,

  the RCSB report seems to indicate an ideal (dictionary) value of 108.3, very close to the monomer library value of 108.4. So the refined values are a couple of degrees away from ideal. Given that this angle is between the base and the ribose it might be worth looking at the pucker of the ribose ring. Alternatively, if you have good resolution it might be that these are reasonable values - note that the ESD for this angle defined in the monomer library is 3.0, while the validation analysis performed at the RCSB seems to use 0.3. 

  Cheers,
	Paul

On Jan 5, 2011, at 12:00 PM, Scott Classen wrote:

> Hello,
> 
> I'm running into validation problems with DNA when validating on PDB website.
> 
> the validation report indicates that the refined value is significantly different that the PDBs standard dictionary.
> 
> Deviation  Residue  Chain  Sequence  AT1  -  AT2  -  AT3    Bond    Dictionary  Standard
>             Name     ID     Number                          Angle      Value    Deviation
> -------------------------------------------------------------------------------------------
>     2.2     DG       D        6      N9   -  C1'  -  O4'    110.5     108.3        0.3
>     2.6     DC       D        7      N1   -  C1'  -  O4'    110.9     108.3        0.3
>     2.3     DC       D        8      N1   -  C1'  -  O4'    110.6     108.3        0.3
>     3.0     DT       D        9      N1   -  C1'  -  O4'    111.3     108.3        0.3
> 
> I've looked through a few of these in the .geo file and it appears that phenix.refine is using different values.
> 
> for example,
> 
> angle pdb=" O4'  DG D   6 "
>      pdb=" C1'  DG D   6 "
>      pdb=" N9   DG D   6 "
>    ideal   model   delta    sigma   weight residual
>   108.40  110.18   -1.78 3.00e+00 1.11e-01 3.52e-01
> 
> 
> ideal is specified as 108.4º so clearly my refinement has converged, but it has NOT converged on the RCSBs accepted value of 110.5º
> 
> What to do? Who is "right" phenix or RCSB?
> 
> Thanks,
> Scott
> 
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Paul Adams
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