23. SHELXD requires the user to supply an exact space group for
direct methods and is therefore unlikely to yield a reasonable
solution if the user’s prediction is incorrect. Conversely,
SHELXT extracts the Laue symmetry of the indexing solution
and determines the space group through multiple considerations [39]. Depending on the number of atoms, solutions with
a combined figure of merit (CFOM) greater than 80 will have a
high probability of being correct (Fig. 5).
24. Programs such as SHELXLE require manual input of electron
scattering factors as SFAC commands [40]. Due to artefacts
unique to electron diffraction, the R-factors of refined
MicroED structures generally exceed those of their X-ray
counterparts. An acceptable solution could exhibit R work and
R free values near or less than 0.25, with a split below 0.05
(Fig. 6b).
Acknowledgments
We thank Drs. Duilio Cascio, Marcus Gallagher-Jones, and Ms. Lee
Joon Kim (UCLA) for careful reading of this chapter and for their
insightful comments and discussion. This work is supported by the
STROBE National Science Foundation Science & Technology
Center, Grant No. DMR-1548924, DOE Grant DE-FC0202ER63421 and NIH-NIGMS Grant R35 GM128867. A.S. is
supported as an NSF Graduate Research Fellow under Grant
No. DGE-1650604. C.Z. is supported by a UCLA dissertation
year fellowship. J.A.R. is supported as a Searle Scholar, a Pew
Scholar, a Packard Fellow and a Beckman Young Investigator.
References
1. Shi D, Nannenga BL, de la Cruz MJ et al
(2016) The collection of MicroED data for
macromolecular crystallography. Nat Protoc
11:895–904
2. Shi D, Nannenga BL, Iadanza MG et al (2013)
Three-dimensional electron crystallography of
protein microcrystals. elife 2:e01345
3. Rodriguez JA, Eisenberg DS, Gonen T (2017)
Taking the measure of MicroED. Curr Opin
Struct Biol 46:79–86
4. Jones CG, Martynowycz MW, Hattne J et al
(2018) The cryoEM method MicroED as a
powerful tool for small molecule structure
determination. ACS Cent Sci 4:1587–1592
5. Rodriguez JA, Ivanova MI, Sawaya MR et al
(2015) Structure of the toxic core of
α-synuclein from invisible crystals. Nature
525:486–490
6. Sawaya MR, Rodriguez J, Cascio D et al
(2016) Ab initio structure determination
from prion nanocrystals at atomic resolution
by MicroED. PNAS 113(40):11232–11236
7. Zee C, Glynn C, Gallagher-Jones M et al
(2019) Homochiral and racemic MicroED
structures of a peptide repeat from the
ice-nucleation protein InaZ. IUCrJ 6:1502238
8. Gallagher-Jones M, Glynn C, Boyer DR et al
(2018) Sub-a ˚ngstro ¨m cryo-EM structure of a
prion protofibril reveals a polar clasp. Nat
Struct Mol Biol 25:131–134
9. de la Cruz MJ, Hattne J, Shi D et al (2017)
Atomic-resolution structures from fragmented
protein crystals with the cryoEM method
MicroED. Nat Methods 14:399–402
10. Guenther EL, Cao Q, Trinh H et al (2018)
Atomic structures of TDP-43 LCD segments
MicroED of Small Macromolecules
347
direct methods and is therefore unlikely to yield a reasonable
solution if the user’s prediction is incorrect. Conversely,
SHELXT extracts the Laue symmetry of the indexing solution
and determines the space group through multiple considerations [39]. Depending on the number of atoms, solutions with
a combined figure of merit (CFOM) greater than 80 will have a
high probability of being correct (Fig. 5).
24. Programs such as SHELXLE require manual input of electron
scattering factors as SFAC commands [40]. Due to artefacts
unique to electron diffraction, the R-factors of refined
MicroED structures generally exceed those of their X-ray
counterparts. An acceptable solution could exhibit R work and
R free values near or less than 0.25, with a split below 0.05
(Fig. 6b).
Acknowledgments
We thank Drs. Duilio Cascio, Marcus Gallagher-Jones, and Ms. Lee
Joon Kim (UCLA) for careful reading of this chapter and for their
insightful comments and discussion. This work is supported by the
STROBE National Science Foundation Science & Technology
Center, Grant No. DMR-1548924, DOE Grant DE-FC0202ER63421 and NIH-NIGMS Grant R35 GM128867. A.S. is
supported as an NSF Graduate Research Fellow under Grant
No. DGE-1650604. C.Z. is supported by a UCLA dissertation
year fellowship. J.A.R. is supported as a Searle Scholar, a Pew
Scholar, a Packard Fellow and a Beckman Young Investigator.
References
1. Shi D, Nannenga BL, de la Cruz MJ et al
(2016) The collection of MicroED data for
macromolecular crystallography. Nat Protoc
11:895–904
2. Shi D, Nannenga BL, Iadanza MG et al (2013)
Three-dimensional electron crystallography of
protein microcrystals. elife 2:e01345
3. Rodriguez JA, Eisenberg DS, Gonen T (2017)
Taking the measure of MicroED. Curr Opin
Struct Biol 46:79–86
4. Jones CG, Martynowycz MW, Hattne J et al
(2018) The cryoEM method MicroED as a
powerful tool for small molecule structure
determination. ACS Cent Sci 4:1587–1592
5. Rodriguez JA, Ivanova MI, Sawaya MR et al
(2015) Structure of the toxic core of
α-synuclein from invisible crystals. Nature
525:486–490
6. Sawaya MR, Rodriguez J, Cascio D et al
(2016) Ab initio structure determination
from prion nanocrystals at atomic resolution
by MicroED. PNAS 113(40):11232–11236
7. Zee C, Glynn C, Gallagher-Jones M et al
(2019) Homochiral and racemic MicroED
structures of a peptide repeat from the
ice-nucleation protein InaZ. IUCrJ 6:1502238
8. Gallagher-Jones M, Glynn C, Boyer DR et al
(2018) Sub-a ˚ngstro ¨m cryo-EM structure of a
prion protofibril reveals a polar clasp. Nat
Struct Mol Biol 25:131–134
9. de la Cruz MJ, Hattne J, Shi D et al (2017)
Atomic-resolution structures from fragmented
protein crystals with the cryoEM method
MicroED. Nat Methods 14:399–402
10. Guenther EL, Cao Q, Trinh H et al (2018)
Atomic structures of TDP-43 LCD segments
MicroED of Small Macromolecules
347