Likelihood-based structure solution in Phaser and Phenix By providing three-dimensional pictures of biological molecules, macromolecular crystallography underpins a deeper understanding of the processes that maintain life. As such, it plays a key role in the basic science of biochemistry and molecular biology, as well as the development of new therapies by the pharmaceutical industry. New algorithms, based on the statistical concept of maximum likelihood, will be developed in the program Phaser an6 incorporated in the Phenix package to determine the 3D structures of proteins and nucleic acids more quickly and more automatically. With these new tools, other crystallographers should gain a better return on the investment made in their research, and crystallographic methods should become accessible to researchers with less specialist expertise. The majority of crystal structures are now solved by the technique of molecular replacement, which exploits the known structure of a related molecule. By coupling the sensitivity of likelihood-based molecular replacement in Phaser with sophisticated modeling techniques in the program Rosetta developed by the group of David Baker, the reach of molecular replacement will be further extended to use starting models that are more distantly related than currently feasible. The next most popular method of structure solution is single-wavelength anomalous diffraction (SAD) phasing, which shares with molecular replacement the advantage of requiring data from only one good crystal. The strength of likelihood for phasing, once the positions of the anomalous scatterers are known, will be extended to improving methods for determining the initial substructure. Increased automation in the Phenix package will make advanced algorithms available to novice crystallographers, and will allow expert crystallographers to explore many more possibilities for structure solution. Methods will be developed to exploit a partial solution in one crystal form, either by molecular replacement or experimental phasing, to solve additional crystal forms. Advanced methods will be developed for refining pairs of structures, to give a clearer picture of the differences between them.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-BCMB-H)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Lawrence Berkeley National Laboratory
United States
Zip Code
Bunkóczi, Gábor; McCoy, Airlie J; Echols, Nathaniel et al. (2015) Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nat Methods 12:127-30
Kapral, Gary J; Jain, Swati; Noeske, Jonas et al. (2014) New tools provide a second look at HDV ribozyme structure, dynamics and cleavage. Nucleic Acids Res 42:12833-46
Wall, Michael E; Van Benschoten, Andrew H; Sauter, Nicholas K et al. (2014) Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering. Proc Natl Acad Sci U S A 111:17887-92
Sauter, Nicholas K; Hattne, Johan; Brewster, Aaron S et al. (2014) Improved crystal orientation and physical properties from single-shot XFEL stills. Acta Crystallogr D Biol Crystallogr 70:3299-309
Klei, Herbert E; Moriarty, Nigel W; Echols, Nathaniel et al. (2014) Ligand placement based on prior structures: the guided ligand-replacement method. Acta Crystallogr D Biol Crystallogr 70:134-43
Headd, Jeffrey J; Echols, Nathaniel; Afonine, Pavel V et al. (2014) Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement. Acta Crystallogr D Biol Crystallogr 70:1346-56
Echols, Nathaniel; Morshed, Nader; Afonine, Pavel V et al. (2014) Automated identification of elemental ions in macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 70:1104-14
Parkhurst, James M; Brewster, Aaron S; Fuentes-Montero, Luis et al. (2014) dxtbx: the diffraction experiment toolbox. J Appl Crystallogr 47:1459-1465
Deis, Lindsay N; Pemble 4th, Charles W; Qi, Yang et al. (2014) Multiscale conformational heterogeneity in staphylococcal protein a: possible determinant of functional plasticity. Structure 22:1467-77
Echols, Nathaniel; Moriarty, Nigel W; Klei, Herbert E et al. (2014) Automating crystallographic structure solution and refinement of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 70:144-54

Showing the most recent 10 out of 75 publications