DNA covalent bond angles deviate from PDB standard dictionary
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
Hi Scott,
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
The "ideal" value originates from $PHENIX/chem_data/mon_lib/g/GD.cif which has not changed for many years. I'm very surprised that the PDB is flagging these long-standing CCP4 monomer library values. I suggest you explain to the PDB that the angles in question are expected results. Ralf
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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participants (3)
-
Paul Adams -
Ralf W. Grosse-Kunstleve -
Scott Classen