Utility of B-factors in protein science: interpreting rigidity, flexibility, and internal motion and engineering thermostability

Z Sun, Q Liu, G Qu, Y Feng, MT Reetz - Chemical reviews, 2019 - ACS Publications
The term B-factor, sometimes called the Debye–Waller factor, temperature factor, or atomic
displacement parameter, is used in protein crystallography to describe the attenuation of X …

Macromolecular room temperature crystallography

M Fischer - Quarterly Reviews of Biophysics, 2021 - cambridge.org
X-ray crystallography enables detailed structural studies of proteins to understand and
modulate their function. Conducting crystallographic experiments at cryogenic temperatures …

[PDF][PDF] New tools for the analysis and validation of cryo-EM maps and atomic models

PV Afonine, BP Klaholz, NW Moriarty… - … Section D: Structural …, 2018 - journals.iucr.org
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly
increasing number of atomic models of biomacromolecules that have been solved using this …

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

BA Barad, N Echols, RYR Wang, Y Cheng, F DiMaio… - Nature …, 2015 - nature.com
Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of
validation metrics to independently assess map quality and model geometry. We report …

Accessing protein conformational ensembles using room-temperature X-ray crystallography

JS Fraser, H Van Den Bedem… - Proceedings of the …, 2011 - National Acad Sciences
Modern protein crystal structures are based nearly exclusively on X-ray data collected at
cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little …

A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density

NM Pearce, T Krojer, AR Bradley, P Collins… - Nature …, 2017 - nature.com
In macromolecular crystallography, the rigorous detection of changed states (for example,
ligand binding) is difficult unless signal is strong. Ambiguous ('weak'or 'noisy') density is …

Hidden alternative structures of proline isomerase essential for catalysis

JS Fraser, MW Clarkson, SC Degnan, R Erion, D Kern… - Nature, 2009 - nature.com
A long-standing challenge is to understand at the atomic level how protein dynamics
contribute to enzyme catalysis. X-ray crystallography can provide snapshots of …

Alternate states of proteins revealed by detailed energy landscape mapping

MD Tyka, DA Keedy, I André, F DiMaio, Y Song… - Journal of molecular …, 2011 - Elsevier
What conformations do protein molecules populate in solution? Crystallography provides a
high-resolution description of protein structure in the crystal environment, while NMR …

Ligand binding remodels protein side-chain conformational heterogeneity

SA Wankowicz, SH de Oliveira, DW Hogan… - Elife, 2022 - elifesciences.org
While protein conformational heterogeneity plays an important role in many aspects of
biological function, including ligand binding, its impact has been difficult to quantify …

Modelling dynamics in protein crystal structures by ensemble refinement

BT Burnley, PV Afonine, PD Adams, P Gros - elife, 2012 - elifesciences.org
Single-structure models derived from X-ray data do not adequately account for the inherent,
functionally important dynamics of protein molecules. We generated ensembles of structures …