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

Reply via email to