Paper Citing NAMD - Abstract
des Georges, Amedee; Hashem, Yaser; Buss, Sarah N.; Jossinet, Fabrice; Zhang, Qin; Liao, Hstau Y.; Fu, Jie; Jobe, Amy; Grassucci, Robert A.; Langlois, Robert; Bajaj, Chandrajit; Westhof, Eric; Madison-Antenucci, Susan; Frank, Joachim
High-resolution Cryo-EM Structure of the Trypanosoma brucei Ribosome: A Case Study
COMPUTATIONAL METHODS FOR THREE-DIMENSIONAL MICROSCOPY RECONSTRUCTION, 97-132, 2014
Single-particle cryo-electron microscopy has the immense advantage over crystallography in being able to image frozen-hydrated biological complexes in their "native" state, in solution. For years the ribosome has been the benchmark sample for particles without symmetry. It has witnessed steady improvement in resolution from the very first single-particle 3D reconstruction to today's reconstructions at near-atomic resolution. In this study, we describe the different steps of sample preparation, data collection, data processing, and modeling that led to the 5 structure of the T. brucei ribosome [32]. A local resolution estimation demonstrates the extent to which resolution can be anisotropic and pinpoints regions of higher heterogeneity or structural flexibility. This study also shows an example of misuse of spatial frequency filters leading to overfitting of the data and the artifacts that can be observed in the resulting density map.
