Dear Oliver, Since you mentioned my name let me try to confuse the issue. The iron atoms in Fe4S4 clusters can adopt different oxidation states, e.g. in HiPIPs and Ferrodoxins, and one might expect this to influence the geometry of the clusters. So maybe you would need several different sets of restraints. However at the time most of these structures were determined, the influence of radiation damage was generally underestimated. In general the first thing that happens in a synchrotron beam is that the clusters mop up the electrons released by the action of the radiation and so they probably had lower oxidation states than the people determining the structures (at least this one) thought that they had. What we should have done was to try to get a Moessbauer spectrum of each crystal before and after the data collection, but it is easy to say that now and anyway the crystals were probably too small.
Best wishes, George > > The dictionaries I sent have values that are obtained from an analysis of > small > molecule crystal structures in the CSD (by "hand" with conquest). For > instance > the Fe-Scluster-Fe angle has a mean of 73.4 degree with a standard > deviation > of 0.7 degrees. The restraints are compatible with Engh and Huber restraints > you > will be using for your protein and for that matter the Parkinson et al > restraints used > for any nucleic acid (because they come from a similar data mining > procedure). > So if Stephen used this dictionary he would not " introduce a bias in the > final rms > angle deviation value" because the restraint values would be sensible. > > If you to check the restraint values are sensible then you check them > against atomic > resolution structures for instance > http://www.rcsb.org/pdb/explore/explore.do?structureId=1B0Y > at 0.93 Å resolution structure determined by George Sheldrick. This has SF4 > with > Fe-Scluster-Fe angles around 73.3 degrees. > > I would strongly advise anyone against using a restraint dictionary for > Fe4S4 that uses > 90 degree as the ideal angle because you are restraining towards values that > > make no sense. If the dictionary contains chiral volume terms then I would > ask the > question why? But this is just my personal take. > > If CCP4 would like to redistribute/work the dictionaries sent then we would > be happy > (please email off-list). > > Dr Oliver Smart > Director SmartSci Limited http://www.smartsci.uk/ > & Consultant Global Phasing Ltd http://www.globalphasing.com/ > -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
