Anomalous Scattering Signal (anomalous + scattering_signal)

Distribution by Scientific Domains

Selected Abstracts

Away from the edge II: in-house Se-SAS phasing with chromium radiation

Hao Xu
Recently, the demands of high-throughput macromolecular crystallography have driven continuous improvements in phasing methods, data-collection protocols and many other technologies. Single-wavelength anomalous scattering (SAS) phasing with chromium X-ray radiation opens a new possibility for phasing a protein with data collected in-house and has led to several successful examples of de novo structure solution using only weak anomalous scatterers such as sulfur. To further reduce data-collection time and make SAS phasing more robust, it is natural to combine selenomethionine-derivatized protein (SeMet protein) with Cr,K, radiation to take advantage of the larger anomalous scattering signal from selenium ( = 2.28 e,) compared with sulfur ( = 1.14 e,). As reported herein, the crystal structure of a putative chorismate mutase from Clostridium thermocellum was determined using Se-SAS with Cr,K, radiation. Each protein molecule contains eight selenomethionine residues in 148 amino-acid residues, providing a calculated Bijvoet ratio of about 3.5% at the Cr,K, wavelength. A single data set to 2.2, resolution with approximately ninefold redundancy was collected using an imaging-plate detector coupled with a Cr source. Structure solution, refinement and deposition to the Protein Data Bank were performed within 9,h of the availability of the scaled diffraction data. The procedure used here is applicable to many other proteins and promises to become a routine pathway for in-house high-throughput crystallography. [source]

Monitoring the anomalous scattering signal and noise levels in X-ray diffraction of crystals

Zheng-Qing Fu
A statistical index Ras is proposed in order to monitor the overall signal-to-noise ratio in an anomalous scattering data set. In this approach, symmetry-equivalent reflections are merged and grouped into centric and non-centric subsets. Reflections in the centric subset, which in theory should be equal, are used to estimate the noise level in the data. This approach differs from that used by most data-processing programs, in which the centric reflections are merged and averaged. By preserving the differences in centric reflections during data processing, an internal measure of the noise level can be estimated and used to analyze the quality of the anomalous signal in the data. An index Ras is defined as the ratio of the average Bijvoet difference of merged acentric reflections to merged centric reflections. Test results on a variety of data show that Ras has good correlation with the capability to determine the anomalous scattering substructure from the data. Ras can also be useful in monitoring the quality of the data in terms of the data-collection strategy, instrument settings and data-processing software used. Ras analysis has been implemented in the program 3DSCALE as part of a data-processing program suite that is under development in our laboratory. [source]

Novel approach to phasing proteins: derivatization by short cryo-soaking with halides

Zbigniew Dauter
A quick (less than 1,min) soak of protein crystals in a cryo-solution containing bromide or iodide anions leads to incorporation of these anomalous scatterers into the ordered solvent region around the protein molecules. These halide anions provide a convenient way of phasing through their anomalous scattering signal: bromides using multiwavelength anomalous dispersion (MAD) and bromides and/or iodides using single-wavelength anomalous dispersion (SAD) or single isomorphous replacement with anomalous scattering (SIRAS) methods. This approach has been tested successfully on four different proteins and has been used to solve the structure of a new protein of molecular weight 30,kDa. [source]

Use of thallium to identify monovalent cation binding sites in GroEL

Philip D. Kiser
GroEL is a bacterial chaperone protein that assembles into a homotetradecameric complex exhibiting D7 symmetry and utilizes the co-chaperone protein GroES and ATP hydrolysis to assist in the proper folding of a variety of cytosolic proteins. GroEL utilizes two metal cofactors, Mg2+ and K+, to bind and hydrolyze ATP. A K+ -binding site has been proposed to be located next to the nucleotide-binding site, but the available structural data do not firmly support this conclusion. Moreover, more than one functionally significant K+ -binding site may exist within GroEL. Because K+ has important and complex effects on GroEL activity and is involved in both positive (intra-ring) and negative (inter-ring) cooperativity for ATP hydrolysis, it is important to determine the exact location of these cation-binding site(s) within GroEL. In this study, the K+ mimetic Tl+ was incorporated into GroEL crystals, a moderately redundant 3.94, resolution X-ray diffraction data set was collected from a single crystal and the strong anomalous scattering signal from the thallium ion was used to identify monovalent cation-binding sites. The results confirmed the previously proposed placement of K+ next to the nucleotide-binding site and also identified additional binding sites that may be important for GroEL function and cooperativity. These findings also demonstrate the general usefulness of Tl+ for the identification of monovalent cation-binding sites in protein crystal structures, even when the quality and resolution of the diffraction data are relatively low. [source]