Re: [ccp4bb] weekend puzzle
Thanks to all who engaged with my little puzzle. The weekend is over and I'm not exactly closer to fitting the right pieces into the density. Benzamidine was a good suggestion for the first bit of density. However, I didn't use that inhibitor during purification. The second set of blobs doesn't sit on a twofold. It might just remain undefined. Thanks anyway for all replies. Andreas On 13/09/13 17:50, Andreas Förster wrote: Dear all, a structure I'm refining is enjoying a free R factor of 18 but still suffers from mystery density that nothing in the crystallization condition could explain. I can't explain it either. Maybe you like to venture some guesses? The missing ligand is derivatized benzoic acid, nitrobenzene or benzamide. I didn't find anything obvious in the PDB. Any suggestions? http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle1.png The second ligand is a longer shot, two blobs connected by a substantial bridge. The two views are slightly rotated, and a bit of peptide is shown to give an idea of the size. http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle2.png http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle3.png Happy guessing! -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London
[ccp4bb] weekend puzzle
Dear all, a structure I'm refining is enjoying a free R factor of 18 but still suffers from mystery density that nothing in the crystallization condition could explain. I can't explain it either. Maybe you like to venture some guesses? The missing ligand is derivatized benzoic acid, nitrobenzene or benzamide. I didn't find anything obvious in the PDB. Any suggestions? http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle1.png The second ligand is a longer shot, two blobs connected by a substantial bridge. The two views are slightly rotated, and a bit of peptide is shown to give an idea of the size. http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle2.png http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle3.png Happy guessing! Andreas -- Andreas Förster Crystallization and Xray Facility Manager Centre for Structural Biology Imperial College London
Re: [ccp4bb] weekend puzzle
On 13/09/13 17:50, Andreas Förster wrote: Dear all, a structure I'm refining is enjoying a free R factor of 18 but still suffers from mystery density that nothing in the crystallization condition could explain. I can't explain it either. Maybe you like to venture some guesses? The missing ligand is derivatized benzoic acid, nitrobenzene or benzamide. I didn't find anything obvious in the PDB. Any suggestions? http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle1.png The second ligand is a longer shot, two blobs connected by a substantial bridge. The two views are slightly rotated, and a bit of peptide is shown to give an idea of the size. http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle2.png http://www.msf.bio.ic.ac.uk/images/puzzle/puzzle3.png Happy guessing! This is what I can detect from your images... it's not really a nugget, is it? It's more of a splat. (it *is* Friday afternoon, that's my excuse...:)) Paul. attachment: Screenshot-Coot Ligand Builder.png
