Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F+ and F−, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

/pdf/phaser-crystallographic-software-2ceb03fha6.pdf

Phaser crystallographic software

Iterative dual-space direct methods based on phase refinement in reciprocal space and peak picking in real space are able to locate relatively large numbers of anomalous scatterers efficiently from MAD or SAD data. Truncation of the data at a particular resolution, typically in the range 3.0–3.5 A, can be critical to success. The efficiency can be improved by roughly an order of magnitude by Patterson-based seeding instead of starting from random phases or sites; Patterson superposition methods also provide useful validation. The program SHELXD implementing this approach is available as part of the SHELX package.

Substructure solution with SHELXD.

Refined crystal structure of Cd, Zn metallothionein at 2.0Åresolution

https://mcl1.ncifcrf.gov/dauter_pubs/176.pdf

Anomalous signal of solvent bromides used for phasing of lysozyme.

Procedures are described for normalizing structure-factor difference magnitudes, |Δ|F||SIR = ||FDer| − |FNat|| ≤ |FHeavy| or |Δ|F||SAS = ||F+h| − |F−h|| ≤ 2|F′′|, to prepare data for probabilistic direct methods phasing to determine heavy-atom or anomalous-scattering substructures in SIR (single-derivative isomorphous replacement) or SAS (single-wavelength anomalous scattering) cases. Applications of the procedures in several recent determinations of multi-selenium substructures in selenomethionyl proteins via SnB direct-methods phasing are briefly summarized.

Difference structure‐factor normalization for heavy‐atom or anomalous‐scattering substructure determinations

Observed anomalous scattering differences have been used with the direct-methods program MULTAN87 to determine the positions of anomalous scatterers in a variety of metalloproteins and a small molecule. The lack of anomalous differences in the centric data did not prevent the determination of the atom positions and the anomalous scatterers were found in all cases. These results show that the method may be useful to determine the positions of anomalous scatterers in the case of multi-site genetically engineered proteins.

http://journals.iucr.org/a/issues/1989/10/00/bw0576/bw0576.pdf

A.K. Mukherjee

Papers

The use of MULTAN to locate the positions of anomalous scatterers