[phenixbb] DNA covalent bond angles deviate from PDB standard dictionary
Scott Classen
sclassen at lbl.gov
Wed Jan 5 12:00:41 PST 2011
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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