Hi Everybody,
I have a problem refining the Ethyl mercurys in my structure. My
working
& free Rs are 16.6% & 19.9% respectively and the geometry of the protein
is very good for this 1.7A MAD structure. However, I see fairly large
negative peaks (greater than 5 sigma) on the mercurys, surrounded by
by dumbell shaped positive density below it. This is after numerous
rounds of positional & b refinement & one round of occupancy refinement.
I suspect that this has something to do with the scattering factor I am
selecting for the mercury. As far as I can figure out HG+2 is the
appropriate ion for an ethyl mercury bonded to a cysteinyl sulfur. Am
I wrong? If not, does anyone have any idea what else the problem could
be?Following are the topology & parameter files I am using for the
mercury:
topology:
set echo=false end
MASS HG+2 200.59000 ! assuming HG -> 200.59000 + 1.008 * 0 (Hs)
MASS CX2 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
MASS CX3 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
autogenerate angles=true end
RESIdue EHG
GROUp
ATOM HG TYPE HG+2 CHARge 1.0 END ! Nr of Hs = 0
ATOM C1 TYPE CX2 CHARge 0.0 END ! Nr of Hs = 1
ATOM C2 TYPE CX3 CHARge 0.0 END ! Nr of Hs = 2
BOND HG C1
BOND C1 C2
ANGLE HG C1 C2
END { RESIdue EHG }
PRESidue HGSC {patch residue for Cys - Ethg}
GROUp
MODIfy ATOM 2CB TYPE=CH2E CHARGE=0.00 END
MODIfy ATOM 2SG TYPE=SH1E CHARge=-1.00 END
ADD BOND 1HG 2SG
ADD ANGLE 2CB 2SG 1HG
ADD ANGLE 2SG 1HG 1C1
END
parmeter:
Remarks Parameters for residue type EHG
set echo=false end
BOND SH1E HG+2 200.0 2.374 ! from CSD; Nobs = 33; probe=C-Hg-S-C
BOND HG+2 CX2 1000.0 2.021 ! Nobs = 1
BOND CX2 CX3 1000.0 1.462 ! Nobs = 1
ANGLE CH2E SH1E HG+2 40.0 100.1 ! from CSD; Nobs = 33; probe=C-Hg-S-C
ANGLE SH1E HG+2 CX2 40.0 175.7 ! from CSD; Nobs = 33; probe=C-Hg-S-C
ANGLe HG+2 CX2 CX3 500.0 108.45 ! Nobs = 1
! NONBonded HGX1 0.0 0.00 0.00 0.00 ! >>> WARNING - No data for Mercury;
set yourself
NONBonded HG+2 0.0450 3.385 0.0450 3.385 ! Using Sn values from
parameter.elements
NONBonded CX2 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
NONBonded CX3 0.1200 3.7418 0.1000 3.3854 ! assuming Carbon
Any help will really be appreciated.
Thanks,
Sangita.
sangita at bragg.bio.purdue.edu
