Application of sulfur SAD to small crystals with a large asymmetric unit and anomalous substructure

The application of sulfur single-wavelength anomalous dispersion (S-SAD) to determine the crystal structures of macromolecules can be challenging if the asymmetric unit is large, the crystals are small, the size of the anomalously scattering sulfur structure is large and the resolution at which the anomalous signals can be accurately measured is modest. Here, as a study of such a case, approaches to the SAD phasing of orthorhombic Ric-8A crystals are described. The structure of Ric-8A was published with only a brief description of the phasing process [Zeng et al. (2019), Structure, 27, 1137 – 1141]. Here, alternative approaches to determining the 40-atom sulfur substructure of the 103   kDa Ric-8A dimer that composes the asymmetric unit are explored. At the data-collection wavelength of 1.77   Å measured at the Frontier micro-focusing Macromolecular Crystallography (FMX) beamline at National Synchrotron Light Source II, the sulfur anomalous signal strength, | Δ ano|/ σ Δ ano (d ′ ′ /sig), approaches 1.4 at 3.4   Å resolution. The highly redundant, 11   000   000-reflection data set measured from 18 crystals was segmented into isomorphous clusters using BLEND in the CCP4 program suite. Data sets within clusters or sets of clusters were scaled and merged using AIMLESS from CCP4 or, alternatively, the phenix.scale_and_merge tool from the Phenix suite. The latter proved to be the more effective in extracting anomalous signals. The HySS tool in Phenix, SHELXC/...

Source: Acta Crystallographica Section D - July 14, 2022 Category: Biochemistry Authors: Mou, T.-C. Zeng, B. Doukov, T.I. Sprang, S.R. Tags: sulfur SAD phasing data scaling single-wavelength anomalous dispersion sulfur substructure determination large asymmetric unit Ric-8A research papers Source Type: research