[phenixbb] Refinement

Tim Gruene tg at shelx.uni-ac.gwdg.de
Tue May 26 14:27:50 PDT 2015


Dear mohamed noor,

in X-ray refinement one electron this way or the other would not make much
difference until you are working with data in the charge density region (below,
say 0.6A).
At normal resolution ranges you cannot distinguish really between N, C, O, so
for Fe with three times as many electrons, +2 or +3 wouldn't have much effect.

Best,
Tim


On Sat, May 23, 2015 at 07:01:01AM +0100, mohamed noor wrote:
> Sorry to bring up an old thread. While tidying up my model before
> deposition, I noticed that in eLBOW, the HEM restraint has a charge of 0
> for the Fe atom. Shouldn't this be +2 or +3? Usually Fe atom gets reduced
> by X-ray anyway. Or does this only matter for those doing molecular
> dynamics?
> 
> On Tue, Mar 31, 2015 at 10:21 PM, Edward A. Berry <BerryE at upstate.edu>
> wrote:
> 
> >
> >
> > On 03/31/2015 02:12 PM, Pavel Afonine wrote:
> > ~~~~~~~~~~~~~~~~
> >
> >> In fact, the C atom is covalently linked to the nearest Cys, so the
> >>> HEM side chain should be 'moved' into the density and the green blob
> >>> shouldn't be there.
> >>>
> >>
> >> Is this link defined anywhere in restraints used in refinement?
> >>
> >> Pavel
> >>
> >
> > Here is an example of restraints for heme c.
> > Values are from the high-resolution structure 1C75.
> > Here residue 501 is the heme of course; and 37, 40, 41, and 160 are
> > the C,C,H, and M in CxxCH---M heme c binding motif.
> > I use HEC.cif for the heme parameters, but make sure the bond lengths
> > in the vinyl groups are consistent with single bonds.
> >
> >   geometry_restraints.edits {
> >      bond {
> >       action = *add delete change
> >       atom_selection_1 = chain D and resid 501 and name FE
> >       atom_selection_2 = chain D and resid 41 and name NE2
> >       symmetry_operation = None
> >       distance_ideal = 1.99
> >       sigma = 0.1
> >       slack = None
> >     }
> >     bond {
> >       action = *add delete change
> >       atom_selection_1 = chain D and resid 501 and name FE
> >       atom_selection_2 = chain D and resid 160 and name SD
> >       symmetry_operation = None
> >       distance_ideal = 2.33
> >       sigma = 0.1
> >       slack = None
> >     }
> >     bond {
> >       action = *add delete change
> >       atom_selection_1 = chain D and resname CYS and resid 37 and name SG
> >       atom_selection_2 = chain D and resname HEC and resid 501 and name CAB
> >       symmetry_operation = None
> >       distance_ideal = 1.815
> >       sigma = 0.1
> >       slack = None
> >     }
> >     bond {
> >       action = *add delete change
> >       atom_selection_1 = chain D and resname CYS and resid 40 and name SG
> >       atom_selection_2 = chain D and resname HEC and resid 501 and name CAC
> >       symmetry_operation = None
> >       distance_ideal = 1.815
> >       sigma = 0.1
> >       slack = None
> >     }
> >
> >
> >
> >
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-- 
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
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