Performance Analysis and Optimization of Cyro-EM Structure Determination in RELION-2

Lipids containing long polymethylene chains were among the first compounds subjected to electron diffraction structure analysis. It was only recently realized, however, that various distortions of thin lipid microcrystal plates, e.g. bends, polar group and methyl end plane disorders, etc. (1-3), restrict coherent scattering to the methylene subcell alone, particularly if undistorted molecular layers have well-defined end planes. Thus, ab initio crystal structure determination on a given single uncharacterized natural lipid using electron diffraction data can only hope to identify the subcell packing and the chain axis orientation with respect to the crystal surface. In lipids based on glycerol, for example, conformations of long chains and polar groups about the C-C bonds of this moiety still would remain unknown.One possible means of surmounting this difficulty is to investigate structural analogs of the material of interest in conjunction with the natural compound itself. Suitable analogs to the glycerol lipids are compounds based on the three configurational isomers of cyclopentane-1,2,3-triol shown in Fig. 1, in which three rotameric forms of the natural glycerol derivatives are fixed by the ring structure (4-7).

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Simulated Dark-Field Electron Micrographs of Point Defects and Organometallics

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100114621 ◽

1975 ◽

Vol 33 ◽

pp. 200-201

Author(s):

William Krakow

Keyword(s):

Electron Micrographs ◽

Point Defects ◽

Structure Determination ◽

Atomic Structure ◽

Image Interpretation ◽

Dark Field ◽

Field Electron ◽

Dark Field Microscopy ◽

Dark Field Electron

Tilted beam dark-field microscopy has been applied to atomic structure determination in perfect crystals, several synthesized molecules with heavy atcm markers and in the study of displaced atoms in crystals. Interpretation of this information in terms of atom positions and atom correlations is not straightforward. Therefore, calculated dark-field images can be an invaluable aid in image interpretation.

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Profile Imaging of Silicon Surface Reconstructions

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100118229 ◽

1985 ◽

Vol 43 ◽

pp. 262-263

Author(s):

O.L. Krivanek ◽

G.J. Wood

Keyword(s):

Electron Microscopy ◽

Surface Structure ◽

Structure Determination ◽

Silicon Surface ◽

Good Resolution ◽

Surface Reconstructions ◽

Bulk Structure ◽

Point To Point ◽

The Relationship

Electron microscopy at 0.2nm point-to-point resolution, 10-10 torr specimei region vacuum and facilities for in-situ specimen cleaning presents intere; ing possibilities for surface structure determination. Three methods for examining the surfaces are available: reflection (REM), transmission (TEM) and profile imaging. Profile imaging is particularly useful because it giv good resolution perpendicular as well as parallel to the surface, and can therefore be used to determine the relationship between the surface and the bulk structure.

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A study on α-RuCl3 crystal structure by scanning tunneling microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100152124 ◽

1989 ◽

Vol 47 ◽

pp. 30-31

Author(s):

H.-J. Cantow ◽

H. Hillebrecht ◽

S. Magonov ◽

H. W. Rotter ◽

G. Thiele

Keyword(s):

Crystal Structure ◽

Density Distribution ◽

Scanning Tunneling Microscopy ◽

Electron Density ◽

Structure Determination ◽

Electron Density Distribution ◽

Scanning Tunneling ◽

Monoclinic Space Group ◽

Tunneling Microscopy ◽

X Ray

From X-ray analysis, the conclusions are drawn from averaged molecular informations. Thus, limitations are caused when analyzing systems whose symmetry is reduced due to interatomic interactions. In contrast, scanning tunneling microscopy (STM) directly images atomic scale surface electron density distribution, with a resolution up to fractions of Angstrom units. The crucial point is the correlation between the electron density distribution and the localization of individual atoms, which is reasonable in many cases. Thus, the use of STM images for crystal structure determination may be permitted. We tried to apply RuCl3 - a layered material with semiconductive properties - for such STM studies. From the X-ray analysis it has been assumed that α-form of this compound crystallizes in the monoclinic space group C2/m (AICI3 type). The chlorine atoms form an almost undistorted cubic closed package while Ru occupies 2/3 of the octahedral holes in every second layer building up a plane hexagon net (graphite net). Idealizing the arrangement of the chlorines a hexagonal symmetry would be expected. X-ray structure determination of isotypic compounds e.g. IrBr3 leads only to averaged positions of the metal atoms as there exist extended stacking faults of the metal layers.

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Are HOLZ lines kinematic in off-zone-axis orientation?

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100149295 ◽

1993 ◽

Vol 51 ◽

pp. 692-693

Author(s):

J. M. Zuo ◽

A. L. Weickenmeier ◽

R. Holmestad ◽

J. C. H. Spence

Keyword(s):

Structure Determination ◽

Standard Procedure ◽

High Order ◽

Zone Axis ◽

Great Promise ◽

Line Position ◽

Measured Intensity ◽

Constant Intensity ◽

Axis Orientation ◽

Diffraction Condition

The application of high order reflections in a weak diffraction condition off the zone axis center, including those in high order laue zones (HOLZ), holds great promise for structure determination using convergent beam electron diffraction (CBED). It is believed that in this case the intensities of high order reflections are kinematic or two-beam like. Hence, the measured intensity can be related to the structure factor amplitude. Then the standard procedure of structure determination in crystallography may be used for solving unknown structures. The dynamic effect on HOLZ line position and intensity in a strongly diffracting zone axis is well known. In a weak diffraction condition, the HOLZ line position may be approximated by the kinematic position, however, it is not clear whether this is also true for HOLZ intensities. The HOLZ lines, as they appear in CBED patterns, do show strong intensity variations along the line especially near the crossing of two lines, rather than constant intensity along the Bragg condition as predicted by kinematic or two beam theory.

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