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
- 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
- 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
- Sheldrick G.M. A short history of SHELX. Acta Crystallographica A. 2008;64:112–122. doi: 10.1107/S0108767307043930
- 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
- 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
- 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
- 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
- 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
- Spence J.C.H. XFELs for structure and dynamics in biology. IUCrJ. 2017;4:322–339. doi: 10.1107/S2052252517005760
- Standfuss J., Spence J. Serial crystallography at synchrotrons and X-ray lasers. IUCrJ. 2017;4:100–101. doi: 10.1107/S2052252517001877
- 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
- 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
- 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
- Landau L.D., Lifshitz E.M. Mechanics, 3d edition. Butterworth-Heinemann; 1976. 224 p.
- Landau L.D., Lifshitz E.M. The Classical Theory of Fields, 4th edition. Butterworth-Heinemann; 1980. 402 p.
- 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
- 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
- Rudin W Functional analysis. McGRAW-HILL BOOK COMPANY, 1973.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Sayre D. Some implications of a theorem due to Shannon. Acta Crystallographica. 1952;5:843. doi: 10.1107/S0365110X52002276
- 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
- Bricogne G. Methods and programs for direct-space exploitation of geometric redundancies. Acta Crystallographica A. 1976;32:832–847. doi: 10.1107/S0567739476001691
- 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.
- 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).
- 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
- 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
- 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
|
|
|