Phasing at high resolution using Ta₆Br₁₂cluster

Abstract

The Ta 6 Br 2 12 cluster compound is known to be a powerful reagent for derivatization of crystals of large macromolecules at low resolution. The cluster is a regular octahedron of six Ta atoms with 12 bridging Br atoms at the edges of the octahedron. The cluster is compact, of approximately spherical shape, with a radius of about 6 A Ê . Both tantalum and bromine display a signi®cant anomalous diffraction signal at their absorption edges at 1.25 and 0.92 A Ê , respectively. At resolutions lower than 5 A Ê the tantalum cluster behaves as a super-atom and provides very large isomorphous and anomalous signals, which signi®cantly diminish at about 4 A Ê . However, beyond 3 A Ê the individual Ta atoms can be resolved and the phasing power of the cluster increases again. The Ta 6 Br 2 12 cluster has been used for phasing four different proteins at high resolution. Ta 6 Br 2 12 appeared to be a mild derivatization reagent and, despite partial incorporation, led to a successful solution of crystal structures by the singlewavelength anomalous diffraction (SAD) approach.

Crystallization and preliminary X-ray diffraction analysis of the human XRCC4–XLF complex

“…This may reflect the very large asymmetric unit and the high degree of structural similarity between XRCC4 and XLF. Tantalum bromide has been well documented as a heavy-metal cluster that is suitable for determining the phase of low-resolution structures (Knä blein et al, 1997;Ban et al, 1999;Banumathi et al, 2002;Pomeranz Krummel et al, 2009). Therefore, we attempted to obtain tantalum bromide derivatives by soaking crystals at varying concentrations and for different lengths of time with and without back-soaking.…”

“…Two of these proteins, XRCC4 and XLF, have no known enzymatic function yet are essential for repair, as shown by XLF À/À and XRCC4 À/À mammalian cells, which display severe defects in DSB repair (Giaccia et al, 1990;Zha et al, 2007). XLF and XRCC4 have been shown to directly interact with one another and are responsible for stimulating ligase IV to repair DNA ends (Ahnesorg et al, 2006;Tsai et al, 2007).…”

The crystal structure of yeast copper thionein: The solution of a long-lasting enigma

“…On the other hand, the large anomalous signal coming from the copper cluster (Ϸ20% of the diffracted intensities) could not be straightforwardly used to solve the structure. Metal clusters present in proteins have been used on several occasions to obtain phases exploiting either the isomorphous or the anomalous effect or both (38)(39)(40)(41). It is interesting to note that the large anomalous effect comes from the global scattering of the cluster as a whole: in this sense, the cluster can be used as a group scatterer, and it can yield phases up to a resolution corresponding to Ϸ60-70% of the average diameter of the cluster itself, thus Ϸ5-8 Å.…”

Estimation of anomalous signal in diffraction data

“…If anomalous scatterers form a group (e.g. a disulfide or a metal cluster), this changes the dependence of the anomalous signal on resolution (Banumathi et al, 2003). However, the theoretical predictions may have only a little practical value.…”