Even with the famous waters on "true" Wyckoff positions, I usually observe an elongated or even partly split density, suggesting that the water is disordered, being sometimes closer to one monomer, sometimes closer to the symmetry-related monomer. Since the position of proteins in a crystal is in general not determined by a single water-mediated hydrogen bond, the water will in general not be able to make perfect hydrogen bonds to both symmetry-related monomers at the same time. I think therefore that even waters should generally be considered to be disordered and only in exceptional cases will occupy "true" Wyckoff positions.
Best, Herman -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Ian Tickle Sent: Thursday, December 09, 2010 3:35 PM To: [email protected] Subject: Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms > cases out there (and so far I have heard of a disulfide bond on a > 2-fold connecting two homodimers). I'm slightly puzzled by this example. If the S-S bond is on the special position, then the rest of the molecule can't have 2-fold symmetry, so would have to be rotationally disordered with occupancy = 0.5 to avoid clashing with its symmetry mate: * X -- C * \ * S | S * \ * C -- X * where the *'s indicate the 2-fold axis (i.e. vertically in the plane of the page). In this case, for the reasons I gave in my previous post there's no reason for the disordered S atoms to be exactly on the 2-fold; it would be pure coincidence if they were. If you mean instead that the 2-fold is _perpendicular_ to the S-S bond (i.e. coming straight out of the page in the diagram), the molecule does indeed have 2-fold symmetry and can be ordered with occupancy = 1, but then the S atoms are not on special positions, so this would not be an example of protein atoms _on_ a special position. One could imagine an example, say where the same side-chain on each monomer is cross-linked (e.g. LYS with glutaraldehyde), forming the homodimer: X -- C -- N = C -- C -- C -- C -- C = N -- C -- X Here the central C atom could be on a 2-fold (i.e. axis perpendicular to the page) special position without rotational disorder. I've no idea whether such a structure actually exists! Cheers -- Ian
