Hi Ansuman,
I think that the refinement is putting the atoms in the right place so
there is no 'exploding', 1.8 to 1.9A is the ideal length for Mg-F. Even
though you did not add Mg, if it is required for catalysis there must be
some around and this would then recruited into the MgF3-. As there is
not very much, it looks to me like the occupancy is low - reflected both
in the negative peak and the way the density looks. Unfortunately, it is
very hard to distinguish between Al and Mg but it looks very much to me
like you have MgF3- bound here. Best wishes, Matt.
On 17/01/2015 19:41, ansuman biswas wrote:
Dear Matthew,
I did not add Mg to the crystallization condition. Although, Mg is
required for the catalysis. But I added MgF3 and carried out the
refinement only to find out a negative density around Mg and again it
was exploded (fig). The ideal Al-F bond length is around 1.65A in
AlF3. I downloaded several AlF3 bound structures and found that the
bond length varies from 1.65A to 1.8A. And when I measured the broken
bond distance between Al and F, it came out around 1.8A. I did prepare
a cif file using that AlF3 and refined, only to find out an exploded
AlF3.
Also, no such warning, mentioning the actual bond length, is there in
the log file of Refmac.
regards,
Ansuman
On Saturday, 17 January 2015 8:51 PM, Matthew BOWLER <mbow...@embl.fr>
wrote:
Dear Ansuman,
I agree with Matthew that the refinement seems to be OK - the reason the
bonds are longer is because what you actually have bound is MgF3- and
not AlF3. MgF3- is a much better transition state analogue as it is
isosteric and isoelectronic with a transferring phosphoryl group. At pH
values above ~7.5 Al precipitates out as AlOH and this leaves Mg to fill
the gap. AlF3 does exist as a species but it is octahedral and not
trigonal bipyramidal and has a water molecule occupying the missing F.
There are plenty of MgF structures in the PDB and the MgF bond length is
around 1.9A so I am pretty sure this is the species that you have bound.
Hope this helps, best wishes, Matt.
On 2015-01-16 20:07, ansuman biswas wrote:
> Dear users,
>
> I have a data at 2.2 A resolution. I am able to model AlF3 into the
> electron density (fig attached). However after one cycle of refinement
> the AlF3 molecule is exploding and the atoms move apart (fig2).
>
> AlF3 is already present in refmac library. First, I used that. But it
> broke up after refinement.
>
> Then, I extracted AlF3 coordinate from already published PDB and
> prepared the cif file. But, it also failed. I modified the cif file by
> changing the bond lengths according to the broken AlF3 structure but
> it was of no help.
>
> Kindly suggest how to carry out the refinement.
>
> regards,
> Ansuman
--
Matthew Bowler
Synchrotron Crystallography Group
European Molecular Biology Laboratory
71 avenue des Martyrs
CS 90181 F-38042 Grenoble
France
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