Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.

By P. Rosenthal, R. Henderson. 2003

2,390 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Structural Biology

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Citations in the corpus

The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands (2022, positive): “The postprocessing yielded a map at global resolution of 3.3 Å, sharpened with B-factor of -157.95 Å 2 , according to the FSC = 0.143 criterion (Rosenthal and Henderson, 2003).”
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “The map– model FSC is the correlation between the Fourier coefficients computed by Fourier transformation of the 3D reconstruction and of a model-based map (Rosenthal & Henderson, 2003).”
Induction of Potent Neutralizing Antibody Responses by a Designed Protein Nanoparticle Vaccine for Respiratory Syncytial Virus (2019, methodology): “143 criterion (Rosenthal and Henderson, 2003) and Fourier shell correlation curves were corrected for the effects of soft masking by high-resolution noise substitution (Chen et al.”
New tools for automated high-resolution cryo-EM structure determination in RELION-3 (2018, methodology): “The script then automatically generated a B-fac-tor plot according to Rosenthal and Henderson ( Rosenthal and Henderson, 2003 ), where 1 = d 2 , with d being the resolution of each refinement, is plotted against the logarithm of the number of particles in the subset.”
RELION: Implementation of a Bayesian approach to cryo-EM structure determination (2012, background): “As suggested by Rosenthal and Henderson (2003), upon convergence, the FSC curve is modified as FSC 1⁄4 ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi 2FSCðmÞ=ð1þ FSCðmÞÞ p to esti-”
New tools for the analysis and validation of cryo-EM maps and atomic models (2018, methodology): “1a) the cut-off 0.143 (Rosenthal & Henderson, 2003) has been applied in most cases to estimate dFsc.”
One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions (2013, methodology): “Furthermore, the same information can be used to determine the equivalent B-factors and to sharpen the reconstruction in a localized manner, following available methods (Fernandez et al., 2008; Rosenthal and Henderson, 2003) that use resolution curves to determine optimum parameters.”
FREALIGN: high-resolution refinement of single particle structures. (2007, methodology): “In some studies it was found that the second strategy is more successful in identifying the correct orientation of particles (Rosenthal and Henderson, 2003).”
Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy (2016, methodology): “Reported resolutions were based on the gold-standard FSC = 0.143 criterion 20, 21 , and FSC curves were corrected for the effects of soft masking by high-resolution noise substitution 65 .”
Linking crystallographic model and data quality (2012, positive): “Eqn 3 has been used in electron microscopy studies for a similar purpose (14), and is also related to the Spearman-Brown prophecy formula used in psychometrics to predict what test length is required to achieve a certain level of reliability (15).”
Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6 (2015, methodology): “At low resolution (special frequencies larger than 1/10 Å), the new data sets should therefore emulate data that would have been obtained by a particle of half the mass, that is, 350 kDa, while at higher resolution (special frequencies smaller than 1/10 Å) the data should approximate the signal expe”