In-House Zinc SAD Phasing at Cu Kα Edge

Kim, Min Kyu; Lee, Sang‐Min; An, Young Jun; Jeong, Chang-Sung; Ji, Chang Jun; Lee, Jinwon; Shin, Sun Mi

doi:10.1007/s10059-013-0074-1

Cited by 10 publications

(7 citation statements)

References 61 publications

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“…Three iodine atoms suitable for anomalous dispersion phasing are arranged in an equilateral triangle and are thus easily identifiable in the substructure (Beck et al, 2008(Beck et al, , 2010. Anomalous scatterers such as halide ions or halogenated fragments have increasingly been exploited for experimental phasing (Dauter & Dauter, 2007;Kim et al, 2013;Liu et al, 2011;Ramagopal et al, 2003;Salgado et al, 2005;Bauman et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity

Gourdoupis

Nasta

Ciofi‐Baffoni

et al. 2019

Acta Crystallogr D Struct Biol

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This article describes the approach used to solve the structure of human IBA57 in-house by 5-amino-2,4,6-triiodoisophthalic acid (I3C) high-energy-remote single-wavelength anomalous dispersion (SAD) phasing. Multiple orientations of the same triclinic crystal were exploited to acquire sufficient real data multiplicity for phasing. How the collection of an in-house native data set and its joint use with the I3C derivative through a SIRAS approach decreases the data multiplicity needed by almost 50% is described. Furthermore, it is illustrated that there is a clear data-multiplicity threshold value for success and failure in phasing, and how adding further data does not significantly affect substructure solution and model building. To our knowledge, this is the only structure present in the PDB that has been solved in-house by remote SAD phasing in space group P1 using only one crystal. All of the raw data used, derived from the different orientations, have been uploaded to Zenodo in order to enable software developers to improve methods for data processing and structure solution, and for educational purposes.

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Section: Introductionmentioning

confidence: 99%

In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity

Gourdoupis

Nasta

Ciofi‐Baffoni

et al. 2019

Acta Crystallogr D Struct Biol

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“…Another technique that has recently ISSN 2059-7983 # 2019 International Union of Crystallography become useful, owing both to synchrotron radiation and to the adaptation of direct methods to macromolecular crystallography, is iodide or bromide SAD/MAD, in which the halides are incorporated into a crystal upon brief crystal soaking in highly concentrated halide solutions (Dauter et al, 2000). Finally, Zn 2+ has been recognized as another useful anomalous scatterer that can be specifically incorporated into crystals by soaking even if the protein of interest is not a known or predicted Zn 2+ -binding protein (Cha et al, 2012;Kim et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Utilizing guanine-coordinated Zn²⁺ ions to determine DNA crystal structures by single-wavelength anomalous diffraction

Hou

Tsodikov

2019

Acta Cryst Sect D Struct Biol

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The experimental phase determination of crystal structures of nucleic acids and nucleic acid-ligand complexes would benefit from a facile method. Even for double-stranded DNA, software-generated models are generally insufficiently accurate to serve as molecular replacement search models, necessitating experimental phasing. Here, it is demonstrated that Zn 2+ ions coordinated to the N7 atom of guanine bases generate sufficient anomalous signal for singlewavelength anomalous diffraction (SAD) phasing of DNA crystal structures. Using zinc SAD, three crystal structures of double-stranded DNA oligomers, 5 0 -AGGGATCCCT-3 0 , 5 0 -GGGATCCC-3 0 and 5 0 -GAGGCCTC-3 0 , were determined. By determining the crystal structure of one of these oligomers, GAGGCCTC, in the presence of Mg 2+ instead of Zn 2+ , it was demonstrated that Zn 2+ is not structurally perturbing. These structures allowed the analysis of structural changes in the DNA on the binding of analogues of the natural product mithramycin to two of these oligomers, AGGGATCCCT and GAGGCCTC. Zinc SAD may become a routine approach for determining the crystal structures of nucleic acids and their complexes with small molecules.

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“…Indeed, in some cases, even weak anomalous signal of sulfur ( f′′ =0.56e - at CuKα) can be used for phasing, as demonstrated in pioneering SAD work on crambin 2 . Similarly, zinc ( f′′ =0.68e - at CuKα) was proposed to be useful for in-house SAD experiments 3 . Perhaps the most impressive result came from the structural genomics project, where iodine ion soaks were systematically used for de novo SAD phasing of datasets collected with CuKα radiation 4 .…”

Section: Introductionmentioning

confidence: 99%

Cadmium SAD phasing at CuKα wavelength

et al. 2019

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Single-wavelength anomalous diffraction (SAD) is the most common method for de novo elucidation of macromolecular structures by X-ray crystallography. It requires an anomalous scatterer in a crystal to calculate phases. A recent study by Panneerselvam et al. emphasized the utility of cadmium ions for SAD phasing at the standard synchrotron wavelength of 1 Å. Here we show that cadmium is also useful for phasing of crystals collected in-house with CuKα radiation. Using a crystal of single-domain antibody as an experimental model, we demonstrate how cadmium SAD can be conveniently employed to solve a CuKα dataset. We then discuss the factors which make this method generally applicable.

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In-House Zinc SAD Phasing at Cu Kα Edge

Cited by 10 publications

References 61 publications

In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity

In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity

Utilizing guanine-coordinated Zn²⁺ ions to determine DNA crystal structures by single-wavelength anomalous diffraction

Cadmium SAD phasing at CuKα wavelength

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In-House Zinc SAD Phasing at Cu Kα Edge

Cited by 10 publications

References 61 publications

In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity

In-house high-energy-remote SAD phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations of the same crystal of human IBA57 to increase the multiplicity

Utilizing guanine-coordinated Zn2+ ions to determine DNA crystal structures by single-wavelength anomalous diffraction

Cadmium SAD phasing at CuKα wavelength

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Utilizing guanine-coordinated Zn²⁺ ions to determine DNA crystal structures by single-wavelength anomalous diffraction