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On the routine use of soft X-rays in macromolecular crystallography. Part III. The optimal data-collection wavelength.

Mueller-Dieckmann C, Panjikar S, Tucker PA, Weiss MS
Acta Crystallogr D Biol Crystallogr 61 1263-72 (2005)
Related entries: 2a7a, 2a7c, 2a7d, 2a7e, 2a7f, 2a7g, 2a7h, 2a7i, 2a7j

Cited: 23 times
EuropePMC logo PMID: 16131760

Abstract

Complete and highly redundant data sets were collected at different wavelengths between 0.80 and 2.65 A for a total of ten different protein and DNA model systems. The magnitude of the anomalous signal-to-noise ratio as assessed by the quotient R(anom)/R(r.i.m.) was found to be influenced by the data-collection wavelength and the nature of the anomalously scattering substructure. By utilizing simple empirical correlations, for instance between the estimated deltaF/F and the expected R(anom) or the data-collection wavelength and the expected R(r.i.m.), the wavelength at which the highest anomalous signal-to-noise ratio can be expected could be estimated even before the experiment. Almost independent of the nature of the anomalously scattering substructure and provided that no elemental X-ray absorption edge is nearby, this optimal wavelength is 2.1 A.

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  1. Computational design of a symmetric homodimer using β-strand assembly. Stranges PB, Machius M, Miley MJ, Tripathy A, Kuhlman B. Proc Natl Acad Sci U S A 108 20562-20567 (2011)
  2. Disulfide isomerase activity of the dynamic, trimeric Proteus mirabilis ScsC protein is primed by the tandem immunoglobulin-fold domain of ScsB. Furlong EJ, Choudhury HG, Kurth F, Duff AP, Whitten AE, Martin JL. J Biol Chem 293 5793-5805 (2018)


Reviews citing this publication (2)

  1. SAD phasing: History, current impact and future opportunities. Rose JP, Wang BC. Arch Biochem Biophys 602 80-94 (2016)
  2. Collection of X-Ray Diffraction Data from Macromolecular Crystals. Dauter Z. Methods Mol Biol 1607 165-184 (2017)

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  1. Structures from anomalous diffraction of native biological macromolecules. Liu Q, Dahmane T, Zhang Z, Assur Z, Brasch J, Shapiro L, Mancia F, Hendrickson WA. Science 336 1033-1037 (2012)
  2. The application of hierarchical cluster analysis to the selection of isomorphous crystals. Giordano R, Leal RM, Bourenkov GP, McSweeney S, Popov AN. Acta Crystallogr D Biol Crystallogr 68 649-658 (2012)
  3. Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection. Bowler MW, Guijarro M, Petitdemange S, Baker I, Svensson O, Burghammer M, Mueller-Dieckmann C, Gordon EJ, Flot D, McSweeney SM, Leonard GA. Acta Crystallogr D Biol Crystallogr 66 855-864 (2010)
  4. FAM3B PANDER and FAM3C ILEI represent a distinct class of signaling molecules with a non-cytokine-like fold. Johansson P, Bernström J, Gorman T, Oster L, Bäckström S, Schweikart F, Xu B, Xue Y, Schiavone LH. Structure 21 306-313 (2013)
  5. Experimental and computational active site mapping as a starting point to fragment-based lead discovery. Behnen J, Köster H, Neudert G, Craan T, Heine A, Klebe G. ChemMedChem 7 248-261 (2012)
  6. High-resolution structure of a papaya plant-defense barwin-like protein solved by in-house sulfur-SAD phasing. Huet J, Teinkela Mbosso EJ, Soror S, Meyer F, Looze Y, Wintjens R, Wohlkönig A. Acta Crystallogr D Biol Crystallogr 69 2017-2026 (2013)
  7. Synchrotron microcrystal native-SAD phasing at a low energy. Guo G, Zhu P, Fuchs MR, Shi W, Andi B, Gao Y, Hendrickson WA, McSweeney S, Liu Q. IUCrJ 6 532-542 (2019)
  8. Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography. Doutch J, Hough MA, Hasnain SS, Strange RW. J Synchrotron Radiat 19 19-29 (2012)
  9. Cloning, expression, purification and crystallization as well as X-ray fluorescence and preliminary X-ray diffraction analyses of human ADP-ribosylhydrolase 1. Kernstock S, Koch-Nolte F, Mueller-Dieckmann J, Weiss MS, Mueller-Dieckmann C. Acta Crystallogr Sect F Struct Biol Cryst Commun 65 529-532 (2009)
  10. Synthesis, photophysical properties and systematic evaluations of new phenanthroimidazole fluorescent probe for bioimaging: Experimental and theoretical study. Krawczyk P, Jędrzejewska B, Pietrzak M, Janek T. J Photochem Photobiol B 166 74-85 (2017)
  11. In-house zinc SAD phasing at Cu Kα edge. Kim MK, Lee S, An YJ, Jeong CS, Ji CJ, Lee JW, Cha SS. Mol Cells 36 74-81 (2013)
  12. Multi-crystal native-SAD phasing at 5 keV with a helium environment. Karasawa A, Andi B, Fuchs MR, Shi W, McSweeney S, Hendrickson WA, Liu Q. IUCrJ 9 768-777 (2022)
  13. Characterization of wax as a potential diffraction intensity standard for macromolecular crystallography beamlines. Brandao-Neto J, Thompson SP, Lennie AR, Ferreira FF, Tang CC. J Synchrotron Radiat 17 53-60 (2010)
  14. Data collection for crystallographic structure determination. Rajashankar K, Dauter Z. Methods Mol Biol 1140 211-237 (2014)
  15. Effect of the Chloro-Substitution on Electrochemical and Optical Properties of New Carbazole Dyes. Krawczyk P, Jędrzejewska B, Seklecka K, Cytarska J, Łączkowski KZ. Materials (Basel) 14 3091 (2021)
  16. Modulation of benzofuran structure as a fluorescent probe to optimize linear and nonlinear optical properties and biological activities. Krawczyk P. J Mol Model 26 272 (2020)
  17. On the routine use of soft X-rays in macromolecular crystallography. Part V. Molecular replacement and anomalous scattering. Unge J, Mueller-Dieckmann C, Panjikar S, Tucker PA, Lamzin VS, Weiss MS. Acta Crystallogr D Biol Crystallogr 67 729-738 (2011)
  18. Optimizing the optical and biological properties of 6-(1H-benzimidazole)-2-naphthalenol as a fluorescent probe for the detection of thiophenols: a theoretical study. Krawczyk P. RSC Adv 10 24374-24385 (2020)
  19. Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae. Chang TH, Hsieh FL, Gu X, Smallwood PM, Kavran JM, Gabelli SB, Nathans J. Proc Natl Acad Sci U S A 120 e2221103120 (2023)


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