INDEX
A
Amyloid ......................................................................... 200
Anisotropies........................................................... 56, 164,
170, 174, 176, 177, 179, 184, 280
Assemblies .......................................................31, 63, 163,
174, 175, 189, 195–198, 209, 211, 215, 329, 334
B
Back-injection method........................................ 229, 234,
236, 252, 254, 255, 261
Bacteria .............................................................. 49, 57–59,
61, 62, 76, 77, 86, 89
C
Carbon-sandwich method .................................. 249, 250,
252, 255, 263
Cell biology .................................................................3, 50
Cellular morphology......................................................... 3
Cryo-electron microscopy (Cryo-EM) .......................3, 7,
48–50, 59, 84, 88, 96, 125, 126, 139, 145–159,
161–185, 189–220, 227–230, 233–240, 242,
247–249, 251, 268, 269, 287, 309, 310, 313
Cryo-electron tomography (Cryo-ET).....................3–21,
25, 26, 28, 49–80, 83–109, 189, 195
Cryo-focused ion beam (FIB) milling ........................... 25
Cryo-sectioning.................................................. 25, 85, 96
Crystals .................................................................... 4, 118,
121, 122, 198, 228–231, 233–237, 239, 240,
242, 243, 248–257, 259–263, 267–281,
287–294, 299–302, 304–306, 309–317, 321,
323–326, 329, 330, 334–336, 339, 340, 342–344
D
Density fitting....................................................... 209, 211
Direct methods ................................................... 330, 332,
337, 339, 340, 346, 347
Doses ..................................................................... 4, 5, 12,
13, 21, 33–35, 46, 73, 84, 98–101, 106, 118, 122,
143, 236, 249, 251, 258–261, 263, 293, 306,
310, 313, 314, 316, 317, 323–325, 335, 342
E
Electron crystallography ..................................... 117, 228,
247, 248, 262, 268, 269
Electron diffraction ............................................. 229, 236,
240, 251, 258, 259, 263, 287, 290, 309, 314,
332, 339, 345, 347
Electron microscopes .................................................4, 26,
117, 125, 126, 129, 130, 138, 161, 230, 236,
249, 258, 267, 287, 300, 306, 310, 316, 321, 330
EMAN2 ................................................................... 26, 28,
40–42, 47, 106, 166
F
Fourier shell correlation (FSC) .......................... 153, 156,
157, 161–167, 170–177, 181–185, 207, 276,
279, 280
H
High-resolution tomography ................. 85, 98, 101, 106
I
Image classification ....................................................... 145
Image processing..................................................... 28, 36,
102, 189, 217, 229, 230, 234, 240, 269, 332,
336, 341
IMOD.................................................................. 8, 13–16,
20, 28, 36, 37, 39, 102–107
In situ structural biology ................................................ 83
Ion channels .................................................................. 247
L
Lamella .............................................................. 50, 54–56,
58, 59, 61, 66–71, 73–77, 79, 80, 89–92
M
Mammalian cells...................................................... 3, 6, 8,
25, 58, 59, 61, 77, 86–88, 91, 108
Membrane proteins............................................. 227–244,
247–263, 267, 268
Tamir Gonen and Brent L. Nannenga (eds.), CryoEM: Methods and Protocols, Methods in Molecular Biology, vol. 2215,
https://doi.org/10.1007/978-1-0716-0966-8, © Springer Science+Business Media, LLC, part of Springer Nature 2021
349
A
Amyloid ......................................................................... 200
Anisotropies........................................................... 56, 164,
170, 174, 176, 177, 179, 184, 280
Assemblies .......................................................31, 63, 163,
174, 175, 189, 195–198, 209, 211, 215, 329, 334
B
Back-injection method........................................ 229, 234,
236, 252, 254, 255, 261
Bacteria .............................................................. 49, 57–59,
61, 62, 76, 77, 86, 89
C
Carbon-sandwich method .................................. 249, 250,
252, 255, 263
Cell biology .................................................................3, 50
Cellular morphology......................................................... 3
Cryo-electron microscopy (Cryo-EM) .......................3, 7,
48–50, 59, 84, 88, 96, 125, 126, 139, 145–159,
161–185, 189–220, 227–230, 233–240, 242,
247–249, 251, 268, 269, 287, 309, 310, 313
Cryo-electron tomography (Cryo-ET).....................3–21,
25, 26, 28, 49–80, 83–109, 189, 195
Cryo-focused ion beam (FIB) milling ........................... 25
Cryo-sectioning.................................................. 25, 85, 96
Crystals .................................................................... 4, 118,
121, 122, 198, 228–231, 233–237, 239, 240,
242, 243, 248–257, 259–263, 267–281,
287–294, 299–302, 304–306, 309–317, 321,
323–326, 329, 330, 334–336, 339, 340, 342–344
D
Density fitting....................................................... 209, 211
Direct methods ................................................... 330, 332,
337, 339, 340, 346, 347
Doses ..................................................................... 4, 5, 12,
13, 21, 33–35, 46, 73, 84, 98–101, 106, 118, 122,
143, 236, 249, 251, 258–261, 263, 293, 306,
310, 313, 314, 316, 317, 323–325, 335, 342
E
Electron crystallography ..................................... 117, 228,
247, 248, 262, 268, 269
Electron diffraction ............................................. 229, 236,
240, 251, 258, 259, 263, 287, 290, 309, 314,
332, 339, 345, 347
Electron microscopes .................................................4, 26,
117, 125, 126, 129, 130, 138, 161, 230, 236,
249, 258, 267, 287, 300, 306, 310, 316, 321, 330
EMAN2 ................................................................... 26, 28,
40–42, 47, 106, 166
F
Fourier shell correlation (FSC) .......................... 153, 156,
157, 161–167, 170–177, 181–185, 207, 276,
279, 280
H
High-resolution tomography ................. 85, 98, 101, 106
I
Image classification ....................................................... 145
Image processing..................................................... 28, 36,
102, 189, 217, 229, 230, 234, 240, 269, 332,
336, 341
IMOD.................................................................. 8, 13–16,
20, 28, 36, 37, 39, 102–107
In situ structural biology ................................................ 83
Ion channels .................................................................. 247
L
Lamella .............................................................. 50, 54–56,
58, 59, 61, 66–71, 73–77, 79, 80, 89–92
M
Mammalian cells...................................................... 3, 6, 8,
25, 58, 59, 61, 77, 86–88, 91, 108
Membrane proteins............................................. 227–244,
247–263, 267, 268
Tamir Gonen and Brent L. Nannenga (eds.), CryoEM: Methods and Protocols, Methods in Molecular Biology, vol. 2215,
https://doi.org/10.1007/978-1-0716-0966-8, © Springer Science+Business Media, LLC, part of Springer Nature 2021
349