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Well...some proteins- including Lysozyme, also have a small hinge motion between the two domains. This can give rise to the "somewhat higher" RMS deviation that you observe in different space groups. In such situations, therefore, the Lesk and Chothia rule of sequence identity vs. RMSD does not strictly hold true- because of the inherent conformational disorder in the molecule. If you were to superimpose the two domains individually, I am sure you will observe lower RMSDs. Shekhar Shekhar C. Mande Centre for DNA Fingerprinting and Diagnostics ECIL Road, Nacharam Hyderabad 500076 INDIA Ph: +91-40-27171442 Fax: +91-40-27155610 Email: [EMAIL PROTECTED] On Tue, 17 Jan 2006, Ed Lattman wrote: > Were some of these crystals frozen and some not? Brian Matthews has > documented significant changes in side chain conformations between > structures done at room temperature and flash frozen from the same > crystal form. > > Ed > > Eaton E. Lattman > Dean of Research and Graduate Education > Professor of Biophysics > Krieger School of Arts and Sciences > JHU > 410 516-8215 voice > 410 516-4100 fax > > On Jan 17, 2006, at 9:40 AM, Richard Gillilan wrote: > > > *** For details on how to be removed from this list visit the *** > > *** CCP4 home page http://www.ccp4.ac.uk *** > > > > > > I was surprised when I compared the high-resolution structures of > > lysozyme grown in three different space groups. The overall > > backbone RMSD were 0.7A. This seems large to me, I remember reading > > somewhere that 0.25A was more typical of identical proteins grown > > by different groups under different conditions. Is anyone aware of > > a systematic comparison of identical proteins in different space > > groups? > > > > When looking for small changes in protein structure induced by > > ligand binding, one should ideally compare like space groups, but > > that is often not possible. The case is strengthened when similar > > changes are seen in different space groups. Does anyone have advice > > to offer on how to separate packing effects from true ligand- > > induced changes in ambiguous cases? > > > > Richard Gillilan > > MacCHESS > >
