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Mercury refinement

Sangita Sinha sangita at bragg.bio.purdue.edu
Fri Feb 26 20:10:16 EST 1999


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



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