One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions

By Giovanni Cardone, J. Bernard Heymann, Alasdair C. Steven. 2013

366 citations recorded by the source corpus.

The resolution of density maps from single particle analysis is usually measured in terms of the highest spatial frequency to which consistent information has been obtained. This calculation represents an average over the entire reconstructed volume. In practice, however, substantial local variations in resolution may occur, either from intrinsic properties of the specimen or for technical reasons such as a non-isotropic distribution of viewing orientations. To address this issue, we propose the use of a space-frequency representation, the short-space Fourier transform, to assess the quality of a density map, voxel-by-voxel, i.e. by local resolution mapping. In this approach, the experimental volume is divided into small subvolumes and the resolution determined for each of them. It is illustrated in applications both to model data and to experimental density maps. Regions with lower-than-average resolution may be mobile components or ones with incomplete occupancy or result from multiple conformational states. To improve the interpretability of reconstructions, we propose an adaptive filtering approach that reconciles the resolution to which individual features are calculated with the results of the local resolution map.

Subfields: Materials Chemistry, Structural Biology, Surfaces, Coatings and Films

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In Materials Chemistry

1. Paul D. Adams
2. Pavel V. Afonine
3. Randy J. Read
4. T. C. Terwilliger
5. Nigel W. Moriarty
6. T. Croll
7. A. McCoy
8. Jane S. Richardson

In Structural Biology

1. T. Croll
2. Tristan Cragnolini
3. Pavel V. Afonine
4. T. C. Terwilliger
5. O. Sobolev
6. Maya Topf
7. Li-Wei Hung
8. Paul D. Adams

In Surfaces, Coatings and Films

1. T. Croll
2. Li-Wei Hung
3. Paul D. Adams
4. J. Beton
5. Maya Topf
6. Bruno P. Klaholz
7. Tristan Cragnolini
8. Thomas Mulvaney

Citations in the corpus

• Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, background): “A ‘local resolution’ is thus assigned to different map regions (Cardone et al., 2013; Kucukelbir et al., 2014).”
• New tools for the analysis and validation of cryo-EM maps and atomic models (2018, background): “The notion of local resolution has been introduced for cryo-EM maps (Cardone et al., 2013; Kucukelbir et al., 2014), which reports on the spatial variability in the resolution of three-dimensional EM reconstructions.”
• Integrating model simulation tools and cryo‐electron microscopy (2022, methodology): “FSC-Q is another scoring function that evaluates the fit of individual atoms, using an approach similar to the assessment of local resolution by FSC. 26 The score essentially evaluates the difference between the local resolution of the experimental cryo-EM map, and the local FSC of the model fit int”