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Python library for assessment of three-dimensional electron microscopy density fits. J Appl
Crystallogr 48:1314–1323
103. Henderson R, Chen S, Chen JZ, Grigorieff N, Passmore LA, Ciccarelli L, Rubinstein JL,
Crowther RA, Stewart PL, Rosenthal PB (2011) Tilt-pair analysis of images from a range of
different specimens in single-particle electron cryomicroscopy. J Mol Biol 413:1028–1046
104. Scheres SH (2010) Classification of structural heterogeneity by maximum-likelihood
methods. Methods Enzymol 482:295–320
105. Elmlund D, Le SN, Elmlund H (2017) High-resolution cryo-EM: the nuts and bolts. Curr
Opin Struct Biol 46:1–6
106. Valle M, Zavialov A, Sengupta J, Rawat U, Ehrenberg M, Frank J (2003) Locking and
unlocking of ribosomal motions. Cell 114:123–134
107. Zhao J, Benlekbir S, Rubinstein JL (2015) Electron cryomicroscopy observation of
rotational states in a eukaryotic V-ATPase. Nature 521:241–245
108. White HE, Orlova EV, Chen S, Wang L, Ignatiou A, Gowen B, Stromer T, Franzmann TM,
Haslbeck M, Buchner J, Saibil HR (2006) Multiple distinct assemblies reveal conformational
flexibility in the small heat shock protein Hsp26. Structure. 14:1197–1204
109. White HE, Saibil HR, Ignatiou A, Orlova EV (2004) Recognition and separation of single
particles with size variation by statistical analysis of their images. J Mol Biol 336:453–460
110. Elad N, Clare DK, Saibil HR, Orlova EV (2008) Detection and separation of heterogeneity
in molecular complexes by statistical analysis of their two-dimensional projections. J Struct
Biol 162:108–120
111. Elad N, Farr GW, Clare DK, Orlova EV, Horwich AL, Saibil HR (2007) Topologies of a
substrate protein bound to the chaperonin GroEL. Mol Cell 26:415–426
112. Scheres SH, Gao H, Valle M, Herman GT, Eggermont PP, Frank J, Carazo JM (2007)
Disentangling conformational states of macromolecules in 3D-EM through likelihood
optimization. Nat Methods 4:27–29
113. Nakane T, Kimanius D, Lindahl E, Scheres SH (2018) Characterisation of molecular
motions in cryo-EM single-particle data by multi-body refinement in RELION. Elife. 7:1–18
114. da Fonseca PC, Morris EP (2015) Cryo-EM reveals the conformation of a substrate analogue
in the human 20S proteasome core. Nat Commun 6:7573
115. Fischer N, Neumann P, Konevega AL, Bock LV, Ficner R, Rodnina MV, Stark H (2015)
Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected
cryo-EM. Nature 520:567–570
400
R. Natesh