We have been trying to deposit our peptide structures with D amino acids in
them They are 15 mers all D, with and L racemate, refined in Refmac 5.8.0107
When we run validation, all the D amino acids have bond length outliers, while
none of the L do. Example from the validation server:
"A bond length (or angle) with jZj > 2 is considered an outlier worth
inspection.
Mol Type Chain Res Link Bond lengths Bond angles
Counts RMSZ #jZj > 2 Counts RMSZ #jZj > 2
1 DLY A 10 - 8,?,? 0.47 0 8,?,? 1.74 2 (25%)
1 DLY A 11 - 4,?,? 1.38 1 (25%) 4,?,? 1.51 1 (25%)
1 DPN A 12 - 11,?,? 1.14 1 (9%) 13,?,? 1.29 2 (15%)
1 DAL A 13 - 4,?,? 0.83 0 4,?,? 2.11 2 (50%)
1 DLY A 14 - 4,?,? 1.19 1 (25%) 4,?,? 2.43 1 (25%)
1 DAL A 15 - 4,?,? 1.55 1 (25%) 4,?,? 2.27 1 (25%)
1 DPN A 16 - 11,?,? 1.97 1 (9%) 13,?,? 1.10 1 (7%)
1 DVA A 17 - 6,?,? 1.03 1 (16%) 7,?,? 1.03 1 (14%)"
etc.
None of the L's have this.
I also downloaded the lib file for D and L Leucine and the bond lengths are
different:
Leu
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
LEU N CA single 1.491 0.021
LEU CA HA single 0.980 0.020
LEU CA CB single 1.530 0.020
LEU CB HB3 single 0.970 0.020
LEU CB HB2 single 0.970 0.020
LEU CB CG single 1.530 0.020
LEU CG HG single 0.970 0.020
LEU CG CD1 single 1.521 0.020
LEU CD1 HD11 single 0.960 0.020
LEU CD1 HD12 single 0.960 0.020
LEU CD1 HD13 single 0.960 0.020
LEU CG CD2 single 1.521 0.020
LEU CD2 HD21 single 0.960 0.020
LEU CD2 HD22 single 0.960 0.020
LEU CD2 HD23 single 0.960 0.020
LEU CA C single 1.525 0.021
LEU C O deloc 1.231 0.020
LEU N H1 single 0.960 0.020
LEU N H2 single 0.960 0.020
LEU N H3 single 0.960 0.020
LEU C OXT deloc 1.231 0.020
and for DLE
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
DLe N CA single 1.455 0.020
DLe CB CA single 1.524 0.020
DLe CA C single 1.500 0.020
DLe CG CB single 1.524 0.020
DLe CD1 CG single 1.524 0.020
DLe CD2 CG single 1.524 0.020
DLe O C deloc 1.250 0.020
DLe C OXT deloc 1.250 0.020
DLe HN N single 0.954 0.020
DLe HA CA single 1.099 0.020
DLe HB1 CB single 1.092 0.020
DLe HB2 CB single 1.092 0.020
DLe HG CG single 1.099 0.020
DLe HD21 CD2 single 1.059 0.020
DLe HD22 CD2 single 1.059 0.020
DLe HD23 CD2 single 1.059 0.020
DLe HD11 CD1 single 1.059 0.020
DLe HD12 CD1 single 1.059 0.020
DLe HD13 CD1 single 1.059 0.020
Has anyone seen this? and how do I refine if the restraints are different for
the enantiomorphs? I doubt ALL the bl's
should be different.
Thanks for your help.
Kenneth A. Satyshur, M.S., Ph.D.
Senior Scientist
University of Wisconsin-Madison
Madison, Wisconsin, 53706
608-215-5207
