8. van Heel M (1982) Detection of objects in
quantum-noise-limited images. Ultramicroscopy 7(4):331–341
9. Saxton WO, Baumeister W (1982) The correlation averaging of a regularly arranged bacterial cell envelope protein. J Microsc 127
(Pt 2):127–138. https://doi.org/10.1111/j.
1365-2818.1982.tb00405.x
10. Rosenthal PB, Henderson R (2003) Optimal
determination of particle orientation, absolute
hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol 333
(4):721–745
11. van Heel M, Schatz M (2005) Fourier shell
correlation threshold criteria. J Struct Biol
151(3):250–262. https://doi.org/10.1016/j.
jsb.2005.05.009
12. Sorzano CO, Vargas J, Oton J, Abrishami V, de
la Rosa-Trevin JM, Gomez-Blanco J, Vilas JL,
Marabini R, Carazo JM (2017) A review of
resolution measures and related aspects in 3D
Electron Microscopy. Prog Biophys Mol Biol
124:1–30.
https://doi.org/10.1016/j.
pbiomolbio.2016.09.005
13. Penczek PA (2010) Resolution measures in
molecular electron microscopy. Methods Enzymol 482:73–100. https://doi.org/10.1016/
S0076-6879(10)82003-8
14. Pettersen EF, Goddard TD, Huang CC,
Couch GS, Greenblatt DM, Meng EC, Ferrin
TE (2004) UCSF Chimera--a visualization system for exploratory research and analysis. J
Comput Chem 25(13):1605–1612. https://
doi.org/10.1002/jcc.20084
15. D’Imprima E, Floris D, Joppe M, Sanchez R,
Grininger M, Kuhlbrandt W (2019) Protein
denaturation at the air-water interface and
how to prevent it. elife 8:e42747. https://doi.
org/10.7554/eLife.42747
16. Dudkina NV, Kudryashev M, Stahlberg H,
Boekema
EJ
(2011)
Interaction
of
complexes I, III, and IV within the bovine
respirasome by single particle cryoelectron
tomography. Proc Natl Acad Sci U S A 108
(37):15196–15200.
https://doi.org/10.
1073/pnas.1107819108
17. Diebolder CA, Faas FG, Koster AJ, Koning RI
(2015) Conical Fourier shell correlation
applied to electron tomograms. J Struct Biol
190(2):215–223. https://doi.org/10.1016/j.
jsb.2015.03.010
18. Baldwin
PR,
Lyumkis
D
(2020)
Non-uniformity of projection distributions
attenuates resolution in cryo-EM. Prog Biophys Mol Biol 150:160–183. https://doi.
org/10.1016/j.pbiomolbio.2019.09.002
19. Noble AJ, Dandey VP, Wei H, Brasch J,
Chase J, Acharya P, Tan YZ, Zhang Z, Kim
LY, Scapin G, Rapp M, Eng ET, Rice WJ,
Cheng A, Negro CJ, Shapiro L, Kwong PD,
Jeruzalmi D, des Georges A, Potter CS, Carragher B (2018) Routine single particle CryoEM
sample and grid characterization by tomography. elife 7:e34257. https://doi.org/10.
7554/eLife.34257
20. Taylor KA, Glaeser RM (2008) Retrospective
on the early development of cryoelectron
microscopy of macromolecules and a prospective on opportunities for the future. J Struct
Biol 163(3):214–223. https://doi.org/10.
1016/j.jsb.2008.06.004
21. Hohn M, Tang G, Goodyear G, Baldwin PR,
Huang Z, Penczek PA, Yang C, Glaeser RM,
Adams PD, Ludtke SJ (2007) SPARX, a new
environment for Cryo-EM image processing. J
Struct Biol 157(1):47–55. https://doi.org/
10.1016/j.jsb.2006.07.003
22. Heymann JB, Belnap DM (2007) Bsoft: image
processing and molecular modeling for electron microscopy. J Struct Biol 157(1):3–18.
https://doi.org/10.1016/j.jsb.2006.06.006
23. Tang G, Peng L, Baldwin PR, Mann DS,
Jiang W, Rees I, Ludtke SJ (2007) EMAN2:
an extensible image processing suite for electron microscopy. J Struct Biol 157(1):38–46.
https://doi.org/10.1016/j.jsb.2006.05.009
24. Tan YZ, Aiyer S, Mietzsch M, Hull JA,
McKenna R, Grieger J, Samulski RJ, Baker
TS, Agbandje-McKenna M, Lyumkis D
(2018) Sub-2 A Ewald curvature corrected
structure of an AAV2 capsid variant. Nat Commun 9(1):3628. https://doi.org/10.1038/
s41467-018-06076-6
25. DiPrimio N, Asokan A, Govindasamy L,
Agbandje-McKenna M, Samulski RJ (2008)
Surface loop dynamics in adeno-associated
virus
capsid
assembly.
J
Virol
82
(11):5178–5189. https://doi.org/10.1128/
jvi.02721-07
26. Zhang C, Konermann S, Brideau NJ, Lotfy P,
Wu X, Novick SJ, Strutzenberg T, Griffin PR,
Hsu PD, Lyumkis D (2018) Structural basis
for the RNA-guided ribonuclease activity of
CRISPR-Cas13d. Cell 175(1):212–223.e217.
https://doi.org/10.1016/j.cell.2018.09.001
27. Polley S, Lyumkis D, Horton NC (2019) Indirect readout of DNA controls filamentation
and activation of a sequence-specific endonuclease. bioRxiv:585943. doi:https://doi.org/
10.1101/585943
28. Scheres SH (2012) RELION: implementation
of a Bayesian approach to cryo-EM structure
186
Sriram Aiyer et al.
quantum-noise-limited images. Ultramicroscopy 7(4):331–341
9. Saxton WO, Baumeister W (1982) The correlation averaging of a regularly arranged bacterial cell envelope protein. J Microsc 127
(Pt 2):127–138. https://doi.org/10.1111/j.
1365-2818.1982.tb00405.x
10. Rosenthal PB, Henderson R (2003) Optimal
determination of particle orientation, absolute
hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol 333
(4):721–745
11. van Heel M, Schatz M (2005) Fourier shell
correlation threshold criteria. J Struct Biol
151(3):250–262. https://doi.org/10.1016/j.
jsb.2005.05.009
12. Sorzano CO, Vargas J, Oton J, Abrishami V, de
la Rosa-Trevin JM, Gomez-Blanco J, Vilas JL,
Marabini R, Carazo JM (2017) A review of
resolution measures and related aspects in 3D
Electron Microscopy. Prog Biophys Mol Biol
124:1–30.
https://doi.org/10.1016/j.
pbiomolbio.2016.09.005
13. Penczek PA (2010) Resolution measures in
molecular electron microscopy. Methods Enzymol 482:73–100. https://doi.org/10.1016/
S0076-6879(10)82003-8
14. Pettersen EF, Goddard TD, Huang CC,
Couch GS, Greenblatt DM, Meng EC, Ferrin
TE (2004) UCSF Chimera--a visualization system for exploratory research and analysis. J
Comput Chem 25(13):1605–1612. https://
doi.org/10.1002/jcc.20084
15. D’Imprima E, Floris D, Joppe M, Sanchez R,
Grininger M, Kuhlbrandt W (2019) Protein
denaturation at the air-water interface and
how to prevent it. elife 8:e42747. https://doi.
org/10.7554/eLife.42747
16. Dudkina NV, Kudryashev M, Stahlberg H,
Boekema
EJ
(2011)
Interaction
of
complexes I, III, and IV within the bovine
respirasome by single particle cryoelectron
tomography. Proc Natl Acad Sci U S A 108
(37):15196–15200.
https://doi.org/10.
1073/pnas.1107819108
17. Diebolder CA, Faas FG, Koster AJ, Koning RI
(2015) Conical Fourier shell correlation
applied to electron tomograms. J Struct Biol
190(2):215–223. https://doi.org/10.1016/j.
jsb.2015.03.010
18. Baldwin
PR,
Lyumkis
D
(2020)
Non-uniformity of projection distributions
attenuates resolution in cryo-EM. Prog Biophys Mol Biol 150:160–183. https://doi.
org/10.1016/j.pbiomolbio.2019.09.002
19. Noble AJ, Dandey VP, Wei H, Brasch J,
Chase J, Acharya P, Tan YZ, Zhang Z, Kim
LY, Scapin G, Rapp M, Eng ET, Rice WJ,
Cheng A, Negro CJ, Shapiro L, Kwong PD,
Jeruzalmi D, des Georges A, Potter CS, Carragher B (2018) Routine single particle CryoEM
sample and grid characterization by tomography. elife 7:e34257. https://doi.org/10.
7554/eLife.34257
20. Taylor KA, Glaeser RM (2008) Retrospective
on the early development of cryoelectron
microscopy of macromolecules and a prospective on opportunities for the future. J Struct
Biol 163(3):214–223. https://doi.org/10.
1016/j.jsb.2008.06.004
21. Hohn M, Tang G, Goodyear G, Baldwin PR,
Huang Z, Penczek PA, Yang C, Glaeser RM,
Adams PD, Ludtke SJ (2007) SPARX, a new
environment for Cryo-EM image processing. J
Struct Biol 157(1):47–55. https://doi.org/
10.1016/j.jsb.2006.07.003
22. Heymann JB, Belnap DM (2007) Bsoft: image
processing and molecular modeling for electron microscopy. J Struct Biol 157(1):3–18.
https://doi.org/10.1016/j.jsb.2006.06.006
23. Tang G, Peng L, Baldwin PR, Mann DS,
Jiang W, Rees I, Ludtke SJ (2007) EMAN2:
an extensible image processing suite for electron microscopy. J Struct Biol 157(1):38–46.
https://doi.org/10.1016/j.jsb.2006.05.009
24. Tan YZ, Aiyer S, Mietzsch M, Hull JA,
McKenna R, Grieger J, Samulski RJ, Baker
TS, Agbandje-McKenna M, Lyumkis D
(2018) Sub-2 A Ewald curvature corrected
structure of an AAV2 capsid variant. Nat Commun 9(1):3628. https://doi.org/10.1038/
s41467-018-06076-6
25. DiPrimio N, Asokan A, Govindasamy L,
Agbandje-McKenna M, Samulski RJ (2008)
Surface loop dynamics in adeno-associated
virus
capsid
assembly.
J
Virol
82
(11):5178–5189. https://doi.org/10.1128/
jvi.02721-07
26. Zhang C, Konermann S, Brideau NJ, Lotfy P,
Wu X, Novick SJ, Strutzenberg T, Griffin PR,
Hsu PD, Lyumkis D (2018) Structural basis
for the RNA-guided ribonuclease activity of
CRISPR-Cas13d. Cell 175(1):212–223.e217.
https://doi.org/10.1016/j.cell.2018.09.001
27. Polley S, Lyumkis D, Horton NC (2019) Indirect readout of DNA controls filamentation
and activation of a sequence-specific endonuclease. bioRxiv:585943. doi:https://doi.org/
10.1101/585943
28. Scheres SH (2012) RELION: implementation
of a Bayesian approach to cryo-EM structure
186
Sriram Aiyer et al.