[phenixbb] Refinement

mohamed noor mohamed.noor34 at gmail.com
Fri May 22 23:01:01 PDT 2015


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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