Stephen,

Robbie advice is 100% correct. Be careful about the naming of the sulphur
atoms (is S1 opposite S4 or next to it). I recall that the distributed CCP4
dictionaries have different atom naming than the PDB chemical components
dictionary.  If this is the problem is that the naming is different this
should result
in large restraint violations that should be appear in the REFMAC output
(others can tell you where).

In general diffraction from Fe S clusters is so strong that the atom
positions
are pretty much determined from the electron density. But in case it helps
I did some work data mining restraints for Fe2S2 and Fe4S4 from CSD
structures (this has to be done manually). Please find attached the
resulting FES.cif and SF4.cif restraint dictionaries (distributed with
BUSTER).

Good luck,

Oliver
-------------------
Dr Oliver Smart
Director SmartSci Limited http://www.smartsci.uk/
& Consultant Global Phasing Ltd http://www.globalphasing.com/

on 10/10/14 5:33 PM, Robbie Joosten <[log in to unmask]> wrote:

> Dear Stephen,
>
> The dictionary is very specific about atom names. If you have them swapped
> (as many PDB entries do). The angle and chiral volume restraints will
wreck
> your cluster. You also need to make sure to provide LINK records to attach
> the cluster to the surrounding cysteines.
>
> HTH,
> Robbie
>
> Sent from my Windows Phone
> ________________________________
> Van: <Stephen Carr>
> Verzonden: 10-10-2014 18:07
> Aan: [log in to unmask]
> Onderwerp: [ccp4bb] Refinement of Iron-sulphur clusters
>
> Dear CCP4 BBers,
>
> I am currently refining a model of a protein containing three iron sulphur
> clusters using Refmac (v5.8.0078) and am getting some unusual results.
One
> of the clusters (3fe 4s) seems to behave resonably and the refined
electron
> density looks very nice.  The atoms in the others clusters (4Fe4S and
> 4Fe3S), however, migrate towards the centre of the cluster producing Fo-Fc
> difference maps with strong negative density at the centre surrounded by
> blobs of positive density where the atoms should be.
>
> I have checkedthe refmac dictionaries and there are entries for each of
the
> clusters, so I shouldn't have to explicitly include a cif file for the
> clusters as an input right?  In fact, when I did try to include a
dictionary
> file for one of the clusters refmac gave a warning message in the log
about
> duplicate monomers dictionaries and it made no difference to the
> refinement/maps anyway.
>
> On checking the refmac log file there is no specific mention that there
are
> hetero-groups in the pdb file and no explicit mention that it is using any
> dictionaries during the refinement.  How can I tell if refmac is
> reading/using the dictionaries?  Also bonds within the clusters are
flagged
> up as outliers and deviating by more than 10 sigma from ideal suggesting
> that they are not getting read?
>
> I realise that something chemically odd could be going on at the centres,
> but if I omit them from the model and calculate maps very strong density
> comes back around where the atoms sat before refinement, so I am pretty
> confident that they are in the right place to start with.
>
> Any help with this problem would be greatly appreciated, I'm sure there is
> something obvious that I am missing but can't see what that is at the
> moment.  It is particularly confusing since one cluster apparently behaves
> while the others do not.  I could, of course, try phenix or buster, but I
> would like to get to the bottom of the problem with refmac if possible.
>
> Thanks very much in advance,
>
> Steve
>
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email [log in to unmask]
> tel 01235 567717
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