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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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Figure 1 Experimental methods used to determine macromolecular structures that are deposited in the PDB. The predominant method is X-ray diffraction, followed by nuclear magnetic resonance (NMR), cryo-EM and neutron diffraction.
Figure 1 Experimental methods used to determine macromolecular structures that are deposited in the PDB. The predominant method is X-ray diffraction, followed by nuclear magnetic resonance (NMR), cryo-EM and neutron diffraction.CC BY · PubMed Central
Figure 2 Annual cryo-EM model depositions now outnumber X-ray model depositions in the resolution range 3.5–5 Å.
Figure 2 Annual cryo-EM model depositions now outnumber X-ray model depositions in the resolution range 3.5–5 Å.CC BY · PubMed Central
Figure 3 Since 2015, cryo-EM depositions have accounted for the majority of large macromolecular structures.
Figure 3 Since 2015, cryo-EM depositions have accounted for the majority of large macromolecular structures.CC BY · PubMed Central
Figure 4 The structure-solution steps for X-ray/neutron crystallography and cryo-EM have nuances for each technique, but the overall workflow is similar. Color code: cryo-EM, gray; X-ray crystallography, green; neutron crystallography, red. As neutron diffraction experiments are typically performed with samples for which the structure is known, the phasing, density modification and model-building steps are not part of the workflow.
Figure 4 The structure-solution steps for X-ray/neutron crystallography and cryo-EM have nuances for each technique, but the overall workflow is similar. Color code: cryo-EM, gray; X-ray crystallography, green; neutron crystallography, red. As neutron diffraction experiments are typically performed with samples for which the structure is known, the phasing, density modification and model-building steps are not part of the workflow.CC BY · PubMed Central
Figure 5 The primary tools for X-ray crystallography in Phenix.
Figure 5 The primary tools for X-ray crystallography in Phenix.CC BY · PubMed Central
Figure 6 The primary tools for cryo-EM in Phenix.
Figure 6 The primary tools for cryo-EM in Phenix.CC BY · PubMed Central
Figure 7 Cryo-EM maps deposited per year for different resolution ranges: better than 3 Å, 3–4 Å, 4–5 Å and worse than 5 Å.
Figure 7 Cryo-EM maps deposited per year for different resolution ranges: better than 3 Å, 3–4 Å, 4–5 Å and worse than 5 Å.CC BY · PubMed Central
Figure 8 Ramachandran φ, ψ plots for the pre-Pro case. (a) The reference distribution of 60 000 well determined pre-Pro residues, with contours that enclose the favored 98% of the data (thin green lines) and that exclude the outliers (thick green lines). (b) A pre-Pro Ramachandran plot in the Phenix GUI for a query structure, showing two labeled outliers in red. Note that pre-Pro is very different from a general case Ramachandran plot.
Figure 8 Ramachandran φ, ψ plots for the pre-Pro case. (a) The reference distribution of 60 000 well determined pre-Pro residues, with contours that enclose the favored 98% of the data (thin green lines) and that exclude the outliers (thick green lines). (b) A pre-Pro Ramachandran plot in the Phenix GUI for a query structure, showing two labeled outliers in red. Note that pre-Pro is very different from a general case Ramachandran plot.CC BY · PubMed Central
Figure 9 Screenshots of the cryo-EM Comprehensive validation tool and a Coot window. Clicking on the item in the table of cis/twisted peptides (highlighted in gray) recenters the Coot window on that peptide.
Figure 9 Screenshots of the cryo-EM Comprehensive validation tool and a Coot window. Clicking on the item in the table of cis/twisted peptides (highlighted in gray) recenters the Coot window on that peptide.CC BY · PubMed Central
Figure 10 The videos on the Phenix tutorials YouTube channel cover the main Phenix programs, refinement strategies and lectures.
Figure 10 The videos on the Phenix tutorials YouTube channel cover the main Phenix programs, refinement strategies and lectures.CC BY · PubMed Central

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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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