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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Liebschner, Dorothee, Afonine, Pavel V., Baker, Matthew L., Bunkóczi, Gábor, Chen, Vincent B., Croll, Tristan I., Hintze, Bradley, Hung, Li-Wei, Jain, Swati, McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert D., Poon, Billy K., Prisant, Michael G., Read, Randy J., Richardson, Jane S., Richardson, David C., Sammito, Massimo D., Sobolev, Oleg V., Stockwell, Duncan H., Terwilliger, Thomas C., Urzhumtsev, Alexandre G., Videau, Lizbeth L., Williams, Christopher J., Adams, Paul D.·2019·Acta Crystallographica Section D Structural Biology
DOI 10.1107/s2059798319011471PMC PMC6778852
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Abstract

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

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Metadata

Authors
Liebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L.-W., Jain, S., McCoy, A. J., Moriarty, N. W., Oeffner, R. D., Poon, B. K., Prisant, M. G., Read, R. J., Richardson, J. S., Richardson, D. C., Sammito, M. D., Sobolev, O. V., Stockwell, D. H., Terwilliger, T. C., Urzhumtsev, A. G., Videau, L. L., Williams, C. J., & Adams, P. D.
Venue
Acta Crystallographica Section D Structural Biology
Publisher
International Union of Crystallography (IUCr)
Published
2019-10-01
Volume
75
Issue
10
Pages
861-877
ISSN
2059-7983
DOI
10.1107/s2059798319011471
PMC
PMC6778852
Cited by
7,953
References
7
Licence
Funders
  • National Institutes of Health (P01GM063210, 1R01GM071939)
  • US Department of Energy (DE-AC02-05CH1123.)
  • Wellcome Trust (209407/Z/17/Z)
  • Horizon 2020 (790122)
  • French Infrastructure for Integrated Structural Biology (ANR-10-INBS-05)

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