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 & Bioinformatics. 2015;10(2):508-525.
doi: 10.17537/2015.10.508.
References
- Miao J., Kirz J., Sayre D. The oversampling phasing method. Acta Crystallographica Section D: Biological Crystallography. 2000;56:1312-1315. doi: 10.1107/S0907444900008970
- Thibault P., Elser V., Jacobsen C., Shapiro D., Sayre D. Reconstruction of a yeast cell from X-ray diffraction data. Acta Crystallographica Section A: Foundations of Crystallography. 2006;62:248-261. doi: 10.1107/S0108767306016515
- Song C., Jiang H., Mancuso A., Amirbekian B., Peng L., Sun R., Shah S.S., Zhou Z.H., Ishikawa T., Miao J. Quantitative Imaging of Single, Unstained Viruses with Coherent X Rays. Physical Review Letters. 2008;101. Article No. 158101. doi: 10.1103/PhysRevLett.101.158101
- Maia F.R.N., Ekeberg T., van der Spoel D., Hajdu J. Journal of Applied Crystallography. 2010;43:1535-1539. doi: 10.1107/S0021889810036083
- Seibert M.M., Ekeberg T, Maia F.R.N.C., Svenda M., Andreasson J., Jönsson O., Odic D., Iwan B., Rocker A., Westphal1 D. et al. Single mimivirus particles intercepted and imaged with an X-ray laser. Nature. 2011;470:78-82. doi: 10.1038/nature09748
- Van der Schot G., Svenda M., Maia F.R.N.C., Hantke M., DePonte D., Seibert M.M., Aquila A., Schulz J., Kirian R., Liang M. et al. Imaging single cells in a beam of live cyanobacteria with an X-ray laser. Nature Communication. 2015;6. Article No 5704. doi: 10.1038/ncomms6704
- Feigin L.A., Svergun D.I. Structure Analysis by Small-Angle X-ray and Neutron Scattering. Shpringer; 1987. doi: 10.1007/978-1-4757-6624-0
- Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., P.E. Bourne P.E. The Protein Data Bank. Nucleic Acids Research. 2000;28:235-242. doi: 10.1093/nar/28.1.235
- 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 Section A: Foundations of Crystallography. 1974;30:349-405. doi: 10.1107/S0567739474010722
- Bricogne G. Methods and programs for direct-space exploitation of geometric redundancies. Acta Crystallographica Section A: Foundations of Crystallography. 1976;32:832-847. doi: 10.1107/S0567739476001691
- 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
- Zhang K.Y.J., Cowtan K.D., Main P. Phase improvement by iterative density modification. In: International Tables for Crystallography. 2012;F:385-400. doi: 10.1107/97809553602060000847
- 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;9(2):543-562. doi: 10.17537/2014.9.543
- 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 Section D: Biological Crystallography. 2016;72. (in press).
- Jordan P., Fromme P., Witt H.T., Klukas O., Saenger W., Krauß N. Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution. Nature. 2001;411:909-917. doi: 10.1038/35082000
- Rossmann M.G., Arnold E. Noncrystallographic symmetry averaging of electron density for molecular-replacement phase refinement and extension. In: International Tables for Crystallography. 2012;F:352-363. doi: 10.1107/97809553602060000842
- Matthews B.M. Solvent content of protein crystals. Journal of Molecular Biology. 1968;33:491-497. doi: 10.1016/0022-2836(68)90205-2
- Weichenberger C.X., Rupp B. Ten years of probabilistic estimates of biocrystal solvent content: new insights via nonparametric kernel density estimate. Acta Crystallographica Section D: Biological Crystallography. 2014;70:1579-1588. doi: 10.1107/S1399004714005550
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