[phenixbb] DNA covalent bond angles deviate from PDB standard dictionary
Paul Adams
pdadams at lbl.gov
Wed Jan 5 13:42:13 PST 2011
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
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
--
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology
Building 64, Room 248
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.
Executive Assistant: Kathleen Moody [ KLMoody at lbl.gov ][ 1-510-495-2506 ]
--
More information about the phenixbb
mailing list