Direct incorporation of experimental phase information in model refinement.

By P. Skubák, G. Murshudov, Navraj S. Pannu. 2004

130 citations recorded by the source corpus.

The incorporation of prior phase information into a maximum-likelihood formalism has been shown to strengthen model refinement. However, the currently available likelihood refinement target using prior phase information has shortcomings; the 'phased' refinement target considers experimental phase information indirectly and statically in the form of Hendrickson-Lattman coefficients. Furthermore, the current refinement target implicitly assumes that the prior phase information is independent of the calculated model structure factor. This paper describes the derivation of a multivariate likelihood function that overcomes these shortcomings and directly incorporates experimental phase information from a single-wavelength anomalous diffraction (SAD) experiment. This function, which simultaneously refines heavy-atom and model parameters, has been implemented in the refinement program REFMAC5. The SAD function used in conjunction with the automated model-building procedures of ARP/wARP leads to a successful solution when current likelihood functions fail in a test case shown.

Subfields: Materials Chemistry, Radiation

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Randy J. Read
2. Paul D. Adams
3. Pavel V. Afonine
4. T. C. Terwilliger
5. A. McCoy
6. G. Murshudov
7. T. Croll
8. Martyn D. Winn

In Radiation

1. Pavel V. Afonine
2. A. McCoy
3. Randy J. Read
4. Paul D. Adams

Citations in the corpus

• Overview of the CCP4 suite and current developments (2011, background): “More recently, it has become possible to refine directly against anomalous data for the cases of SAD (Skubák et al., 2004) and SIRAS (Skubák et al., 2009) without the need for estimated phases and phase probabilities.”
• Crystal structures (2004, unknown): “The SAD probability distribution (Skubák et al., 2004) is obtained from (3) by setting E = 2, M = 2, Ppr( ) = constant and |F1| = |Fo +|, |F2| = |(Fo )*|, F3 = Fc +, F4 = (Fc )*, where F + and F are the structure factors of the Friedel pairs.”
• Recent developments in phasing and structure refinement for macromolecular crystallography (2009, background): “Recently there have been efforts to use phasing targets in structure refinement, thus more correctly accounting for the anomalous scattering and the relationship between structure factors [43].”
• Computational protein design enables a novel one-carbon assimilation pathway (2015, methodology): “Proc Natl Acad Sci USA 107(16):7509–7514.”