S-SWAT (softer single-wavelength anomalous technique): potential in high-throughput protein crystallography

Abstract

The drive for yet higher output of protein crystal structures sustains an interest in streamlining data-collection protocols. Highly organized automated robotics attend to one aspect. The data-collection elapsed time also depends on the number of wavelengths used, the data redundancy and the desired diffraction resolution limit. Synchrotron-radiation beamlines offer a centralized data-collection approach with considerable flexibility of choice of wavelength(s) with high beam intensity and fine collimation. The arrival of automated IPs (imaging plates) and CCDs (charge-coupled devices) with sample freezing has widened the scope for ease of data collection and achieving a high redundancy, the latter at the cost of elapsed time per sample. This paper reports a single-wavelength approach where a large optimized f" signal involving the Xe L1-absorption edge is harnessed. Even with modest data redundancy (7), a high-quality electron-density map was obtained from that single data set when combined with phase improvement methods. Two phasing protocols are compared for the same data set. Resolution extension (to 1.4 A), in this test, was also done but via a second data set. In future, with a tilted detector geometry, full diffraction resolution will be collectable in one experiment on the one beamline. Moreover, careful minimization of beamline Be window thickness on the new Daresbury SRS Multipole Wiggler Beamline 10 will maximize the 2-3 A (softer) wavelength intensity performance specification. The work has application to the harnessing of iodine f" optimized signals and enhanced sulfur f", as well as xenon f", in protein crystallography. This approach, softer-SWAT, should 'swat' many protein structures when it comes online.

SAD at home: solving the structure of oxalate decarboxylase with the anomalous signal from manganese using X-ray data collected on a home source

“…The contribution from sulfur is smaller, having an f HH value of only 0.56 electrons at this wavelength and an estimated Bijvoet ratio of 0.6% based on eight ordered S atoms per asymmetric unit. The overall Bijvoet ratio for the manganese and sulfur together was subsequently estimated to be 1.6% using the formula for mixed anomalous substructure atoms derived by Olczak et al (2003). This is signi®cantly higher than the minimum value of 0.6% required for successful phasing suggested by Wang assuming error-free data (Wang, 1985).…”

Estimation of anomalous signal in diffraction data

“…A very similar criterion is the Bijvoet ratio h|ÁF AE |i/h|F |i, which can be estimated theoretically if the number and f 00 value of the anomalous scatterers are known (Hendrickson & Teeter, 1981;Olczak et al, 2003;Shen et al, 2003;see above). The Bijvoet ratio (similarly to R anom ) increases towards unity if the amplitudes are aberrated with errors and its absolute value is not a good indicator of the anomalous signal (Zwart, 2005).…”

“…If more than one type of anomalous scatterer is present, the equation must be modified (Olczak et al, 2003). According to this formula, the Bijvoet ratio should rise at a higher diffraction angle , since f 00 does not depend on , whereas f o diminishes at high resolution.…”

The use of softer X-rays in the structure elucidation of microporous materials

“…where F þ P and F À P are the hkl and " h h " k k " l l amplitudes of the data measured at the f 00 maximum, and f 00 is the value of f 00 for the anomalous scatterer, at the wavelength of the data collection (Olczak et al, 2003).…”

“…Similarly, there is a contribution to the AD from both Co and Zn, for CoZnPO-CZP, which is the only chiral sample, and here the total AD is given by ðAD , i.e. there is a cross-term contribution to the AD (Olczak et al, 2003). Table 4 shows the component DDs for the contributing elements for all the above microporous samples, and the ADs for the chiral case, CoZnPO-CZP.…”