on 13/10/14 6:33 PM, Pedro Matias <[email protected]> wrote: > In relation to this topic, I'd like to mention that SF4 has replaced FS4 > as the Fe4S4 monomer in the CCP4 monomer library. > > However, the dictionary values for bond lengths and angles are not > correct, and this is especially noticeable when the dictionary is used > in a high-resolution refinement (e.g., 1.05 A). In particular, the > Fe-S-Fe angles are all set to 90 degrees, when in fact some are smaller > and others are larger. > > This introduces a bias in the final rms angle deviation values. Fe4S4 is > a distorted cubane, not a perfect cube. >
Pedro, Yes you are 100% correct 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/
