The Resolution in X-ray Crystallography and Single-Particle Cryogenic Electron Microscopy

Abstract

<jats:p>X-ray crystallography and single-particle analysis cryogenic electron microscopy are essential techniques for uncovering the three-dimensional structures of biological macromolecules. Both techniques rely on the Fourier transform to calculate experimental maps. However, one of the crucial parameters, resolution, is rather broadly defined. Here, the methods to determine the resolution in X-ray crystallography and single-particle analysis are summarized. In X-ray crystallography, it is becoming increasingly more common to include reflections discarded previously by traditionally used standards, allowing for the inclusion of incomplete and anisotropic reflections into the refinement process. In general, the resolution is the smallest lattice spacing given by Bragg’s law for a particular set of X-ray diffraction intensities; however, typically the resolution is truncated by the user during the data processing based on certain parameters and later it is used during refinement. However, at which resolution to perform such a truncation is not always clear and this makes it very confusing for the novices entering the structural biology field. Furthermore, it is argued that the effective resolution should be also reported as it is a more descriptive measure accounting for anisotropy and incompleteness of the data. In single particle cryo-EM, the situation is not much better, as multiple ways exist to determine the resolution, such as Fourier shell correlation, spectral signal-to-noise ratio and the Fourier neighbor correlation. The most widely accepted is the Fourier shell correlation using a threshold of 0.143 to define the resolution (so-called “gold-standard”), although it is still debated whether this is the correct threshold. Besides, the resolution obtained from the Fourier shell correlation is an estimate of varying resolution across the density map. In reality, the interpretability of the map is more important than the numerical value of the resolution.</jats:p>

Size Distribution of Inactivated Tick-Borne Encephalitis Virus Particles Revealed by a Comprehensive Physicochemical Approach

“…According to the TEM data, most virions were structurally intact ( Figure 3 A). Using single particle analysis, we obtained a three-dimensional reconstruction of TBEV with an average resolution of 8.0 Å according to FSC 0.143 criterion [ 25 ] ( Figure 3 B,C). The atomic model of TBEV envelope proteins (PDB: 5O6A) was docked to the obtained electron density map, which allowed us to identify the main structural features.…”

In silico investigations identified Butyl Xanalterate to competently target CK2α (CSNK2A1) for therapy of chronic lymphocytic leukemia

“…In this study the 3D conformers (41,581 in number) of 5820 filtered metabolites were downloaded from PubChem database and docked with the target protein (protein kinase CK2α subunit) to analyze the binding energy (ΔG) and binding affinity (Ki). There are several PDB files for the target protein in the database, but we have chosen PDB I’d: 3PE1 for our study with target protein due to its high resolution and it was available with its native ligand (CX-4945) bound to the catalytic (ATP) active site 29 , 31 , 126 , 127 .…”

Recent Advances in Structural Studies of Cytochrome bd and Its Potential Application as a Drug Target

“…Structural analyses of bacterial cytochrome bd oxidases by means of X-ray crystallography ( Geobacillus thermodenitrificans , pdb IDs 5DOQ & 5IR6, [ 9 ]) and cryo-electron microscopy (cryo-EM) ( Escherichia coli bd -I, pdb IDs 6RKO [ 11 ] and 6RX4 [ 10 ]; Mycobacterium smegmatis , 7D5I [ 12 ]; Mycobacterium tuberculosis , 7NKZ [ 13 ] and E. coli bd -II, 7OSE [ 14 ] and 7OY2 [ 15 ]) have shed light on the architecture of this class of oxidases.With the exception of the Geobacillus structures 5DOQ and 5IR6 that were obtained by X-ray crystallography, all structural data are based on cryo-EM. Resolutions range from 3.8 Å (5IR6, X-ray crystallography) to 2.5 Å (7NKZ, cryo-EM), providing near-atomic details (for a detailed discussion of optical resolutions in X-ray crystallography and cryo-EM, we suggest the work of Dubach and Guskov [ 85 ]). This work has unveiled common features shared by all members of the bd oxidase class that are distinctly different from the members of the HCO and AOX classes.…”