Cryo-EM Part B: 3-D Reconstruction

This volume is dedicated to a description of the instruments, samples, protocols, and analyses that belong to cryo-EM. It emphasizes the relatedness of the ideas, instrumentation, and methods underlying all cryo-EM approaches, which allow practitioners to easily move between them. Within each section, the articles are ordered according to the most common symmetry of the sample to which their methods are applied.

* Includes time-tested core methods and new innovations applicable to any researcher * Methods included are useful to both established researchers and newcomers to the field * Relevant background and reference information given for procedures can be used as a guide

1. Fundamentals of three-dimensional reconstruction from projections

Pawel A. Penczek

2. Image Restoration in Cryo-electron Microscopy

Pawel A. Penczek

3. Resolution measures in molecular electron microscopy

Pawel A. Penczek

4. 3D reconstruction from 2D crystal image and diffraction data

Andreas Schenk, Daniel Castaño-Díez, Bryant Gipson, Marcel Arheit, Xiangyan Zeng, and Henning Stahlberg

5. Fourier-Bessel Reconstruction of Helical Assemblies

David L Stokes, Ruben Diaz & William, J. Rice

6. Reconstruction of Helical Filaments and Tubes

Edward H Egelman

7. Three-Dimensional Asymmetric Reconstruction of Tailed Bacteriophage

Jinghua Tang, Robert S. Sinkovits, and Timothy S. Baker

8. Single Particle Analysis at High Resolution

Yao Cong and Steven J. Ludtke

9. The Orthogonal Tilt Reconstruction method

Andres Leschziner

10. An introduction to maximum-likelihood methods in cryo-EM

Fred J. Sigworth, Peter C. Doerschuk, Jose-Maria Carazo, and Sjors H.W. Scheres

11. Classification of structural heterogeneity by maximum-likelihood methods

Sjors H.W. Scheres

12. Methods for three-dimensional reconstruction of heterogeneous assemblies

Elena V Orlova, Helen R. Saibil

13. Alignment of cryo-electron tomography datasets

Fernando Amat, Daniel Casta˜no-Diez, Albert Lawrence, Farshid Moussavi, Hanspeter Winkler, & Mark Horowitz

14. Correcting for the Ewald sphere in high resolution single particle reconstructions

Grant J Jensen, Peter A. Leong, Xuekui Yu, & Z. Hong Zhou

15. Software Tools For Molecular Microscopy: An Open-Text Wikibook

Bridget Carragher, Neil R. Voss, Clinton S. Potter, & Ross Smith