A Structure is Worth a Thousand Gels
Jul 17, 2010
Bernard has made a couple of his figures from his book “Biomolecular Crystallography” available on the CCP4 wiki. I have been reading through his new book and have been really impressed! The images are related to electron density and touch on the following examples:
- Split side-chain conformations
- Solvent molecules (water, MPD, Mg2+)
- Cis-peptide bond and its electron density
- Covalently modified residues
- Covalent binding of ligands
- Heavy-atom derivatization of a protein
- Additives mediating intermolecular contacts
- The trimeric bacterial outer membrane protein OprP
- Chemically modified lysine residue (Dimethyllysine)
- Se-Met residues and chloride ion
- Glycosylated residues stabilizing homodimer
- Uranium-atom solution and Fourier truncation ripples
Gotta love those Fourier truncation ripples 
Posted by Sean |
Categories: Scientific Publication and Presentation | Tagged: Books, Learning, Macromolecular Crystallography |
matt
July 17th, 2010 at 9:00 PM #
nice,
where did you find the pic of that truncation ripple, btw?
thanks
Sean
July 17th, 2010 at 10:12 PM #
Hi Matt,
I found it in the middle of a structure that I was working on :/
Pavel
July 19th, 2010 at 5:15 PM #
Hi, more examples:
1) CCP4 Newsletter
http://www.ccp4.ac.uk/newsletters/newsletter42/content.html
On the Fourier series truncation peaks at subatomic resolution
Anne Bochow, Alexandre Urzhumtsev
2) Page 43: http://phenix-online.org/presentations/neutron_japan_2009/phenix_japan_part1.pdf
3) Central Ligand in the FeMo-Cofactor Nitrogenase MoFe-Protein at 1.16 Å Resolution: A.
Oliver Einsle, et al. Science, 1696 (2002) 297
4) Page 267 Figure 4:
On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps
P. V. Afonine, V. Y. Lunin, N. Muzet and A. Urzhumtsev
Acta Cryst. (2004). D60, 260-274
Cheers,
Pavel.
–
PHENIX developer
Sean
July 27th, 2010 at 8:01 PM #
Pavel – thanks for the additional resources
Huge fan! Keep up the great work on Phenix!