25. X. Li et al., Electron counting and beam-induced motion correction enable
near-atomic-resolution single-particle cryo-EM. Nat. Methods 10(6), 584–590 (2013)
26. M. Kudryashev, D. Castaño-Díez, H. Stahlberg, Limiting factors in single particle cryo
electron tomography. Comput. Struct. Biotechnol. J. 1(2), 1–6 (2012)
27. J.J. Fernández, S. Li, R.A. Crowther, CTF determination and correction in electron
cryotomography. Ultramicroscopy 106(7), 587–596 (2006)
28. H. Winkler, K.A. Taylor, Focus gradient correction applied to tilt series image data used in
electron tomography. J. Struct. Biol. 143(1), 24–32 (2003)
29. R. Danev, B. Buijsse, M. Khoshouei, J.M. Plitzko, W. Baumeister, Volta potential phase plate
for in-focus phase contrast transmission electron microscopy. Proc. Natl. Acad. Sci. U. S. A.
111(44), 15635–15640 (2014)
30. R. Danev, W. Baumeister, “Cryo-EM single particle analysis with the Volta phase plate,”
eLife 5 (2016)
31. M. Khoshouei, S. Pfeffer, W. Baumeister, F. Förster, R. Danev, “Subtomogram analysis using
the Volta phase plate,” J. Struct. Biol. (2016)
32. S. Asano et al., A molecular census of 26S proteasomes in intact neurons. Science 347(6220),
439–442 (2015)
33. P.A. Penczek, J. Frank, “Resolution in Electron Tomography,” in Electron Tomography, ed.
by J. Frank (Springer, New York, 2007), pp. 307–330
34. M. Radermacher, Three-Dimensional reconstruction of single particles from random and
nonrandom tilt series. J. Electron Microsc. Tech. 9(4), 359–394 (1988)
35. P. Penczek, M. Marko, K. Buttle, J. Frank, Double-tilt electron tomography. Ultramicroscopy
60(3), 393–410 (1995)
36. W. Hoppe, D. Typke, “Three-Dimensional Reconstruction of Aperiodic Objects in Electron
Microscopy,” in Unconventional Electron Microscopy for Molecular Structure Determination,
ed. by W. Hoppe, R. Mason (Vieweg+Teubner Verlag, 1979), pp. 137–190
37. S. Lanzavecchia et al., Conical tomography of freeze-fracture replicas: a method for the study
of integral membrane proteins inserted in phospholipid bilayers. J. Struct. Biol. 149(1), 87–98
(2005)
38. N. Kawase, M. Kato, H. Nishioka, H. Jinnai, Transmission electron microtomography without
the ‘missing wedge’ for quantitative structural analysis. Ultramicroscopy 107(1), 8–15 (2007)
39. R.A. Crowther, L.A. Amos, J.T. Finch, D.J. De Rosier, A. Klug, Three dimensional
reconstructions of spherical viruses by fourier synthesis from electron micrographs. Nature
226(5244), 421–425 (1970)
40. W.O. Saxton, W. Baumeister, M. Hahn, Three-dimensional reconstruction of imperfect
two-dimensional crystals. Ultramicroscopy 13(1–2), 57–70 (1984)
41. K.J. Batenburg et al., 3D imaging of nanomaterials by discrete tomography. Ultramicroscopy
109(6), 730–740 (2009)
42. B.R. Gipson, D.J. Masiel, N.D. Browning, J. Spence, K. Mitsuoka, H. Stahlberg, “Automatic
recovery of missing amplitudes and phases in tilt-limited electron crystallography of
two-dimensional crystals,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 84(1, Pt 1), 11916
(2011)
43. Y. Chen et al., FIRT: Filtered iterative reconstruction technique with information restoration.
J. Struct. Biol. 195(1), 49–61 (2016)
44. Y. Deng, Y. Chen, Y. Zhang, S. Wang, F. Zhang, F. Sun, ICON: 3D reconstruction with
‘missing-information’ restoration in biological electron tomography. J. Struct. Biol. 195(1),
100–112 (2016)
45. X. Zhang, Z. Hong, Zhou, “Limiting factors in atomic resolution cryo electron microscopy:
No simple tricks”. J. Struct. Biol. 175(3), 253–263 (2011)
46. J.G. Galaz-Montoya et al., “Alignment algorithms and per-particle CTF correction for single
particle cryo-electron tomography,” J. Struct. Biol
47. F.K.M. Schur, W.J.H. Hagen, A. de Marco, J.A.G. Briggs, Determination of protein structure
at 8.5 Å resolution using cryo-electron tomography and sub-tomogram averaging. J. Struct.
Biol. 184(3), 394–400 (2013)
280
M. Kudryashev
near-atomic-resolution single-particle cryo-EM. Nat. Methods 10(6), 584–590 (2013)
26. M. Kudryashev, D. Castaño-Díez, H. Stahlberg, Limiting factors in single particle cryo
electron tomography. Comput. Struct. Biotechnol. J. 1(2), 1–6 (2012)
27. J.J. Fernández, S. Li, R.A. Crowther, CTF determination and correction in electron
cryotomography. Ultramicroscopy 106(7), 587–596 (2006)
28. H. Winkler, K.A. Taylor, Focus gradient correction applied to tilt series image data used in
electron tomography. J. Struct. Biol. 143(1), 24–32 (2003)
29. R. Danev, B. Buijsse, M. Khoshouei, J.M. Plitzko, W. Baumeister, Volta potential phase plate
for in-focus phase contrast transmission electron microscopy. Proc. Natl. Acad. Sci. U. S. A.
111(44), 15635–15640 (2014)
30. R. Danev, W. Baumeister, “Cryo-EM single particle analysis with the Volta phase plate,”
eLife 5 (2016)
31. M. Khoshouei, S. Pfeffer, W. Baumeister, F. Förster, R. Danev, “Subtomogram analysis using
the Volta phase plate,” J. Struct. Biol. (2016)
32. S. Asano et al., A molecular census of 26S proteasomes in intact neurons. Science 347(6220),
439–442 (2015)
33. P.A. Penczek, J. Frank, “Resolution in Electron Tomography,” in Electron Tomography, ed.
by J. Frank (Springer, New York, 2007), pp. 307–330
34. M. Radermacher, Three-Dimensional reconstruction of single particles from random and
nonrandom tilt series. J. Electron Microsc. Tech. 9(4), 359–394 (1988)
35. P. Penczek, M. Marko, K. Buttle, J. Frank, Double-tilt electron tomography. Ultramicroscopy
60(3), 393–410 (1995)
36. W. Hoppe, D. Typke, “Three-Dimensional Reconstruction of Aperiodic Objects in Electron
Microscopy,” in Unconventional Electron Microscopy for Molecular Structure Determination,
ed. by W. Hoppe, R. Mason (Vieweg+Teubner Verlag, 1979), pp. 137–190
37. S. Lanzavecchia et al., Conical tomography of freeze-fracture replicas: a method for the study
of integral membrane proteins inserted in phospholipid bilayers. J. Struct. Biol. 149(1), 87–98
(2005)
38. N. Kawase, M. Kato, H. Nishioka, H. Jinnai, Transmission electron microtomography without
the ‘missing wedge’ for quantitative structural analysis. Ultramicroscopy 107(1), 8–15 (2007)
39. R.A. Crowther, L.A. Amos, J.T. Finch, D.J. De Rosier, A. Klug, Three dimensional
reconstructions of spherical viruses by fourier synthesis from electron micrographs. Nature
226(5244), 421–425 (1970)
40. W.O. Saxton, W. Baumeister, M. Hahn, Three-dimensional reconstruction of imperfect
two-dimensional crystals. Ultramicroscopy 13(1–2), 57–70 (1984)
41. K.J. Batenburg et al., 3D imaging of nanomaterials by discrete tomography. Ultramicroscopy
109(6), 730–740 (2009)
42. B.R. Gipson, D.J. Masiel, N.D. Browning, J. Spence, K. Mitsuoka, H. Stahlberg, “Automatic
recovery of missing amplitudes and phases in tilt-limited electron crystallography of
two-dimensional crystals,” Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 84(1, Pt 1), 11916
(2011)
43. Y. Chen et al., FIRT: Filtered iterative reconstruction technique with information restoration.
J. Struct. Biol. 195(1), 49–61 (2016)
44. Y. Deng, Y. Chen, Y. Zhang, S. Wang, F. Zhang, F. Sun, ICON: 3D reconstruction with
‘missing-information’ restoration in biological electron tomography. J. Struct. Biol. 195(1),
100–112 (2016)
45. X. Zhang, Z. Hong, Zhou, “Limiting factors in atomic resolution cryo electron microscopy:
No simple tricks”. J. Struct. Biol. 175(3), 253–263 (2011)
46. J.G. Galaz-Montoya et al., “Alignment algorithms and per-particle CTF correction for single
particle cryo-electron tomography,” J. Struct. Biol
47. F.K.M. Schur, W.J.H. Hagen, A. de Marco, J.A.G. Briggs, Determination of protein structure
at 8.5 Å resolution using cryo-electron tomography and sub-tomogram averaging. J. Struct.
Biol. 184(3), 394–400 (2013)
280
M. Kudryashev