Hello,
I am at a loss on what's going on:
I am refining SeMET containing structure and using REFMAC 5.2.0005 on Linux
and, the same thing happening, using REFMAC 5.5.0070 on Windows.
When MET were modelled, there were no difference peaks anywhere. When I
changed them all to MSE, the large difference density peaks showed up. So
either the protein does not contain SeMet or Refmac somehow uses sulfur
scattering factors during refinement.
I have hard time believing the former because 1) the protein was checked by
mass spec to be correct size for SeMet derivative, 2) the structure was
solved by SAD with all five sites correctly found (196 residues total), 3)
first 50 aa of the protein are identical to a known structure.
This is 2.4A resolution and at this point R/Rfree = 25/29.
Refmac log shows correct scattering factors read out:
SE 17.0006 2.4098 5.8196 0.2726 3.9731 15.2372 4.3543
43.8163 2.8409
The PDB has this for MSE:
ATOM 1140 N MSE A 143 35.708 161.163 13.715 1.00 78.82 N
ATOM 1141 CA MSE A 143 35.995 162.467 13.106 1.00 77.86 C
ATOM 1142 CB MSE A 143 36.307 162.307 11.617 1.00 78.79 C
ATOM 1143 CG MSE A 143 37.755 162.127 11.119 1.00 80.89 C
ATOM 1144 SE MSE A 143 37.503 161.104 9.363 1.00 91.22 SE
ATOM 1145 CE MSE A 143 39.169 160.021 9.696 1.00 86.47 C
ATOM 1146 C MSE A 143 34.709 163.226 13.030 1.00 77.70 C
ATOM 1147 O MSE A 143 34.682 164.436 12.737 1.00 77.33 O
Any clues greatly appreciated!
Dima
