Russian version English version
About the Journal
Editorial Board
Instructions for Authors
Information for Readers and Authors
Current Issue
Archive
Contact Us
Search

Send manuscript
 


Volume 15   Issue 1   Year 2020
Lunin V.Y., Lunina N.L., Petrova T.E.

Mask-Based Approach in Phasing and Restoring of Single-Particle Diffraction Data

Mathematical Biology & Bioinformatics. 2020;15(1):57-72.

doi: 10.17537/2020.15.57.

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. Spence J.C.H. XFELs for structure and dynamics in biology. IUCrJ. 2017;4:322–339. doi: 10.1107/S2052252517005760
  8. Standfuss J., Spence J. Serial crystallography at synchrotrons and X-ray lasers. IUCrJ. 2017;4:100–101. doi: 10.1107/S2052252517001877
  9. 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
  10. 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
  11. 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
  12. 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
  13. Lunin V.Y. Mask-based approach to restoring and phasing single-particle diffraction data. In: 32nd European Crystallographic Meeting, Vienna, Austria, August 18-23: Abstract Booklet. 2019. P. 138.
  14. Lunin V.Y., Lunina N.L., Petrova T.E. Single particle study by X-ray diffraction: Crystallographic approach. Mathematical Biology and Bioinformatics. 2019;14(2):500–516. doi: 10.17537/2019.14.500
  15. 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
  16. Kucukelbir A., Sigworth F.J., Tagare H.D. Quantifying the local resolution of cryo-EM density maps. Nature Methods. 2014;11:63–65. doi: 10.1038/nmeth.2727
  17. Afonine P.V., Klaholz B.P., Moriarty N.W., Poon B.K., Sobolev O.V., Terwilliger T.C., Adams P.D., Urzhumtsev A. Acta Crystallographica D. 2018;74:814–840. doi: 10.1107/S2059798318009324
  18. 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
  19. 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
  20. Sayre D. Some implications of a theorem due to Shannon. Acta Crystallographica. 1952;5:843. doi: 10.1107/S0365110X52002276
  21. 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
  22. Bricogne G. Methods and programs for direct-space exploitation of geometric redundancies. Acta Crystallographica A. 1976;32:832–847. doi: 10.1107/S0567739476001691
  23. Lunin V.Y., Lunina N.L. Repairing of the diffraction pattern in the X-ray free electron laser study of biological particles. Advanced Mathematical Models & Applications. 2018;3:117–127.
  24. Lunin V.Y. Use of the fast differentiation algorithm for phase refinement in protein crystallography. Acta Crystallographica A. 1985;41:551–556. doi: 10.1107/S0108767385001209
  25. Podjarny A.D., Rees B., Urzhumtsev A.G. Density modification in X-ray crystallography. In: Methods in Molecular Biology, Crystallographic Methods and Protocols. Eds. Jones C., Milloy B, Sanderson M.R. Totowa, New Jersey: Humana Press, 1996. P. 205-226. (Methods in Molecular Biology, Vol. 56). doi: 10.1385/0-89603-259-0:205
  26. Zhang K.Y.J., Cowtan K.D., Main P. Phase improvement by iterative density modification. In: International Tables for Crystallography. Vol. F. Eds. Arnold E., Himmel D.M., Rossmann M.G. Chichester: John Wiley and Sons, 2012. P. 385–400. doi: 10.1107/97809553602060000847
  27. Wang B.C. Resolution of phase ambiguity in macromolecular crystallography. Methods in Enzymology. 1985;115:90–111. doi: 10.1016/0076-6879(85)15009-3
  28. Fienup J.R. Reconstruction of an object from the modulus of its Fourier transform. Optics Letters. 1978;3(1):27–29. doi: 10.1364/OL.3.000027
  29. Marchesini S. A unified evaluation of iterative projection algorithms for phase retrieval. Rev. Sci. Instrum. 2007;78. Article No. 011301. doi: 10.1063/1.2403783
  30. Millane R., Lo V.L. Iterative projection algorithms in protein crystallography. I. Theory. Acta Crystallographica A. 2013;69:517–527. doi: 10.1107/S0108767313015249
  31. Abrahams J.P. Bias reduction in phase refinement by modified interference functions: introducing the γ-correction. Acta Crystallographica D. 1997;53:371–376. doi: 10.1107/S0907444996015272
  32. Oslányi G., Sütő A. Ab initio structure solution by charge flipping. Acta Crystallographica A. 2004;60:134–141. doi: 10.1107/S0108767303027569
  33. Maia F.R.N.C., Ekeberg T., Spoel D., Hajdu J. Hawk: the image reconstruction package for coherent X-ray diffractive imaging. J. Applied Crystallography. 2010;43:1535–1539. doi: 10.1107/S0021889810036083
  34. Urzhumtsev A.G. The use of local averaging in analysis of macromolecule images at electron density distribution maps: Preprint. Pushchino, 1985 (in Russ.).
  35. Urzhumtsev A.G., Lunin V.Y., Luzyanina T.B. Bounding a Molecule in a Noisy Synthesis. Acta Crystallographica A. 1989;45:34–39. doi: 10.1107/S0108767388008955
  36. Marchesini S., He H., Chapman H.N., Hau-Riege S.P., Noy A., Howells M.R., Weierstall U., Spence J.H.C. X-ray image reconstruction from a diffraction pattern alone. Phis. Rev. B. 2003;68. Article No. 140101(R). doi: 10.1103/PhysRevB.68.140101
  37. 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
  38. 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
  39. Matthews B.W. Solvent Content of Protein Crystals. Journal of Molecular Biology. 1968;33:491–497. doi: 10.1016/0022-2836(68)90205-2
  40. Weichenberger C.X., Afonine P.V., Kantardjieff K., Rupp B. Acta Crystallographica D. 2015;71:1023–1038. doi: 10.1107/S1399004715006045
  41. 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
  42. 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
  43. Lunin V.Y., Woolfson M.M. Mean Phase Error and the Map Correlation Coefficient. Acta Crystallographica D. 1993;49:530–533. doi: 10.1107/S0907444993005852
  44. Broser M., Gabdulkhakov A., Kern J., Guskov A., Müh F., Saenger W., Zouni A. Crystal structure of monomeric Photosystem II from Thermosynechococcus elongatus at 3.6 Å resolution. J. Biol. Chem. 2010;285:26255–26262. doi: 10.1074/jbc.M110.127589
  45. Jordan P., Fromme P., Witt H.T., Klukas O., Saenger W., Krauß N. Three-dimensional structure of cyanobacterial photosystem I at 2.5 Å resolution. Nature. 2001;411:909–917. doi: 10.1038/35082000
  46. 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
  47. Van Heel M., Schatz M. Fourier shell correlation threshold criteria. J. Struct. Biol. 2005;151:250–262. doi: 10.1016/j.jsb.2005.05.009
  48. Van Heel M., Schatz M. Reassessing the Revolution’s Resolutions. bioRxiv. 2017. Article No. 224402. doi: 10.1101/224402
Table of Contents
Original Article
Math. Biol. Bioinf.
2020;15(1):57-72
doi: 10.17537/2020.15.57
published in English

Abstract (eng.)
Abstract (rus.)
Full text (eng., pdf)
References
Translation into Russian
Math. Biol. Bioinf.
2020, 15(Suppl):t1-t20
doi: 10.17537/2020.15.t1

Full text (rus., pdf)

 
  Copyright IMPB RAS © 2005-2024