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
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