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
