Russian version English version
Volume 14   Issue 2   Year 2019
Lunin V.Y., Lunina N.L., Petrova T.E.

Single Particle Study by X-Ray Diffraction: Crystallographic Approach

Mathematical Biology & Bioinformatics. 2019;14(2):500-516.

doi: 10.17537/2019.14.500.

References

 

  1. Adams P.D., Afonine P.V., Bunkóczi G., Chen V.B., Davis I.W., Echols N., Headd J.J., Hung L.-W., Kapral G.J., Grosse-Kunstleve R.W. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica D. 2010;66:213–221. doi: 10.1107/S0907444909052925
  2. Winn M.D., Ballard C.C., Cowtan K.D., Dodson E.J., Emsley P., Evans P.R., Keegan R.M., Krissinel E.B., Leslie A.G.W., McCoy A. et al. Overview of the CCP4 suite and current developments. Acta Crystallographica D. 2011;67:235–242. doi: 10.1107/S0907444910045749
  3. Sheldrick G.M. A short history of SHELX. Acta Crystallographica A. 2008;64:112–122. doi: 10.1107/S0108767307043930
  4. Bricogne G., Vonrhein C., Flensburg C., Schiltz M., Paciorek W. Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallographica D. 2003;59:2023–2030. doi: 10.1107/S0907444903017694
  5. Blanc E., Roversi P., Vonrhein C., Flensburg C., Lea S.M., Bricogne G. Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Crystallographica D. 2004;60:2210–2221. doi: 10.1107/S0907444904016427
  6. Minor W., Cymborowski M., Otwinowski Z., Chruszcz M. HKL-3000: the integration of data reduction and structure solution–from diffraction images to an initial model in minutes. Acta Crystallographica D. 2006;62:859–866. doi: 10.1107/S0907444906019949
  7. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Research. 2000;28:235–242. doi: 10.1093/nar/28.1.235
  8. Lunin V.Y., Lunina N.L., Petrova T.E. The biological crystallography without crystals. Mathematical Biology and Bioinformatics. 2017;12(1):55–72. doi: 10.17537/2017.12.55
  9. Spence J.C.H. XFELs for structure and dynamics in biology. IUCrJ. 2017;4:322–339. doi: 10.1107/S2052252517005760
  10. Standfuss J., Spence J. Serial crystallography at synchrotrons and X-ray lasers. IUCrJ. 2017;4:100–101. doi: 10.1107/S2052252517001877
  11. Aquila A., Barty A., Bostedt C., Boutet S., Carini G., dePonte D., Drell P., Doniach S., Downing K.H., Earnest T. et al. The linac coherent light source single particle imaging road map. Structural Dynamics. 2015;2. doi: 10.1063/1.4918726
  12. Ayyer K., Geloni G., Kocharyan V., Saldin E., Serkez S., Yefanov O., Zagorodnov I. Perspectives for imaging single protein molecules with the present design of the European XFEL. Structural Dynamics. 2015;2. doi: 10.1063/1.4919301
  13. Daurer B.J., Okamoto K., Bielecki J., Maia F.R.N.C., Muhlig K., Seibert M.M., Hantke M.F., Nettelblad C., Benner W.H., Svenda M. et al. Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. IUCrJ. 2017;4:251–262. doi: 10.1107/S2052252517003591
  14. Landau L.D., Lifshitz E.M. Mechanics, 3d edition. Butterworth-Heinemann; 1976. 224 p.
  15. Landau L.D., Lifshitz E.M. The Classical Theory of Fields, 4th edition. Butterworth-Heinemann; 1980. 402 p.
  16. Urzhumtsev A.G., Lunin V.Y. Introduction to crystallographic refinement of macromolecular atomic models. Crystallography Reviews. 2019;25:164–262. doi: 10.1080/0889311X.2019.1631817
  17. Urzhumtseva L., Klaholz B., Urzhumtsev A. On effective and optical resolutions of diffraction data sets. Acta Crystallographica D. 2013;69:1921–1934. doi: 10.1107/S0907444913016673
  18. Rudin W Functional analysis. McGRAW-HILL BOOK COMPANY, 1973.
  19. Rodriguez J.A., Xu R., Chen C.-C., Huang Z., Jiang H., Chen A.L., Raines K.S., Pryor Jr.A., Nam D., Wiegart L. et al. Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells. IUCrJ. 2015;2:575–583. doi: 10.1107/S205225251501235X
  20. Ekeberg T., Svenda M., Abergel C., Maia F.R. N. C., Seltzer V., Claverie J.-M., Hantke M., Jönsson O., Nettelblad C., van der Schot G. et al. Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser. Physical Review Letters. 2015;114. doi: 10.1103/PhysRevLett.114.098102
  21. Munke A., Andreasson J., Aquila A., Awel S., Ayyer K., Barty A., Bean R.J., Berntsen P., Bielecki J., Boutet S. et al. Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source. Scientific Data. 2016;3. doi: 10.1038/sdata.2016.64
  22. Lunin V.Y., Lunina N.L., Petrova T.E., Baumstark M.W., Urzhumtsev A.G. Mask-based approach to phasing of single-particle diffraction data. Acta Crystallographica D. 2016;72:147–157. doi: 10.1107/S2059798315022652
  23. Lunin V.Y., Lunina N.L., Petrova T.E., Baumstark M.W., Urzhumtsev A.G. Mask-based approach to phasing of single-particle diffraction data. II. Likelihood-based selection criteria. Acta Crystallographica D. 2019;75:79–89. doi: 10.1107/S2059798318016959
  24. Meijering E. A chronology of interpolation: from ancient astronomy to modern signal and image processing. Proceedings of the IEEE. 2002;90:319–342. doi: 10.1109/5.993400
  25. Kotel'nikov V.A. On the transmission capacity of 'ether' and wire in electric communications. Physics-Uspekhi. 2006;49(7):736–744. doi: 10.1070/PU2006v049n07ABEH006160
  26. Sayre D. Some implications of a theorem due to Shannon. Acta Crystallographica. 1952;5:843. doi: 10.1107/S0365110X52002276
  27. Bricogne G. Geometric sources of redundancy in intensity data and their use for phase determination. Acta Crystallographica A. 1974;30:395–405. doi: 10.1107/S0567739474010722
  28. Bricogne G. Methods and programs for direct-space exploitation of geometric redundancies. Acta Crystallographica A. 1976;32:832–847. doi: 10.1107/S0567739476001691
  29. Lunin V.Y., Lunina N.L. Repairing of the diffraction pattern in the X-ray freeelectron laser study of biological particles. Advanced Mathematical Models & Applications. 2018;3:117–127.
  30. Misnovs A., Mishnev A. On phasing of oversampled diffraction data. In: 32-nd European Crystallographic Meeting (Vienna, Austria, 18.-23.08): Book of abstracts. 2019. P. 706. https://ecm2019.org/fileadmin/user_upload/k_ecm2019/images/ Programm/ECM32AbstractBooklet_18.08.2019.pdf (accessed 06.11.2019).
  31. Lunin V.Y., Lunina N.L., Petrova T.E. The use of connected masks for reconstructing the single particle image from X-ray diffraction data. Mathematical Biology and Bioinformatics. 2014;10(Suppl.):t1–t19. doi: 10.17537/2015.10.t1
  32. Lunina N.L., Petrova T.E., Urzhumtsev A.G., Lunin V.Y. The use of connected masks for reconstructing the single particle image from X-ray diffraction data. II. The dependence of the accuracy of the solution on the sampling step of experimental data. Mathematical Biology and Bioinformatics. 2015;10(Suppl.):t56–t72. doi: 10.17537/2015.10.t56
  33. Lunina N.L., Petrova T.E., Urzhumtsev A.G., Lunin V.Y. The Use of Connected Masks for Reconstructing the Single Particle Image from X-Ray Diffraction Data. III. Maximum-Likelihood Based Strategies to Select Solution of the Phase Problem. Mathematical Biology and Bioinformatics. 2018;13(Supl.):t70–t83. doi: 10.17537/2018.13.t70
Table of Contents Original Article
Math. Biol. Bioinf.
2019;14(2):500-516
doi: 10.17537/2019.14.500
published in English

Abstract (eng.)
Abstract (rus.)
Full text (eng., pdf)
References Translation into Russian
Math. Biol. Bioinf.
2019;14(S):t44-t61
doi: 10.17537/2019.14.t44

Full text (rus., pdf)

 

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