In the validation report of pdb deposition I get the error of covalent bond angles to be more than six std off. I refined my solution structure using an simulated annealing protocol in implicit water and using the ff12SB force field. As far as I can see the bond angles are taken from parm99.dat file. Comparing the values for the violated angels in the parm99.dat file with the dictionary angels the PDB validation uses reveals a significant discrepancy.
Specifically I talk about the RNA bond angles O4'-C1'-N9 -- > type OS-CT-N* --> 109.5 (PDB 108.5) and C3'-C2'-C1' --> type CT-CT-CT --> 109.5 (PDB 101.5).
Where are these specific angles in the parm99.dat come from. Since there is no literature mentioned in the parm99.dat file I searched myself and found only a paper from 1996 (New Parameters for the Refinement of Nucleic Acid-Containing Structures). In this publication the angels agree with what PDB validation refers to. Can someone explain me where the amber values come from and maybe why they appear to be significantly off?
Here a part of the output of the PDB validation
==> Covalent Angle Values:
The overall RMS deviation for covalent angles relative to the standard dictionary is 1.5 degrees.
The following table contains a list of the covalent bond angles greater than 6 times standard deviation.
Deviation Residue Chain Sequence Model AT1 − AT2 − AT3 Bond Dictionary Standard
Name ID Number Angle Value Deviation
−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−
4.8 U B 3 1 C1’ − C2’ − C3’ 106.3 101.5 0.8 0.8
4.4 A B 4 1 N9 − C1’ − O4’ 112.9 108.5 0.7 0.7
Thanks very much
Markus
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ETH Zurich
Dr. Markus Blatter
Institute of Molecular Biology & Biophysics
Schafmattstrasse 30, HPP L12
8049 Zurich, Switzerland
phone +41 (0) 44 633 0721
email blatter.mol.biol.ethz.ch
web
http://www.mol.biol.ethz.ch
Private
Hochwachtstrasse 39
8400 Winterthur
mobile +41 (0) 76 488 7078
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Received on Wed Jul 16 2014 - 03:00:03 PDT
