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. 2012 Apr;68(Pt 4):336-43.
doi: 10.1107/S0907444911056071. Epub 2012 Mar 16.

Practical structure solution with ARCIMBOLDO

Dayté Rodríguez  1 , Massimo Sammito, Kathrin Meindl, Iñaki M de Ilarduya, Marianus Potratz, George M Sheldrick, Isabel Usón
Affiliations

Practical structure solution with ARCIMBOLDO

Dayté Rodríguez et al. Acta Crystallogr D Biol Crystallogr. 2012 Apr.

Abstract

Since its release in September 2009, the structure-solution program ARCIMBOLDO, based on the combination of locating small model fragments such as polyalanine α-helices with density modification with the program SHELXE in a multisolution frame, has evolved to incorporate other sources of stereochemical or experimental information. Fragments that are more sophisticated than the ubiquitous main-chain α-helix can be proposed by modelling side chains onto the main chain or extracted from low-homology models, as locally their structure may be similar enough to the unknown one even if the conventional molecular-replacement approach has been unsuccessful. In such cases, the program may test a set of alternative models in parallel against a specified figure of merit and proceed with the selected one(s). Experimental information can be incorporated in three ways: searching within ARCIMBOLDO for an anomalous fragment against anomalous differences or MAD data or finding model fragments when an anomalous substructure has been determined with another program such as SHELXD or is subsequently located in the anomalous Fourier map calculated from the partial fragment phases. Both sources of information may be combined in the expansion process. In all these cases the key is to control the workflow to maximize the chances of success whilst avoiding the creation of an intractable number of parallel processes. A GUI has been implemented to aid the setup of suitable strategies within the various typical scenarios. In the present work, the practical application of ARCIMBOLDO within each of these scenarios is described through the distributed test cases.

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Figures

Figure 1
Figure 1
Scheme showing the alternative process flow and variables and files to be set up to run ARCIMBOLDO.
Figure 2
Figure 2
Placed fragments and resulting map or structure for the test cases. (a) The three three-fragment substructures leading to structure solution in the case of PRD2 when using model helices of 14 alanines. Whereas the helices depicted in red and orange are common to all three solutions, the blue one is slightly different for two of them and partially overlapped and out of density for the third. The resulting electron-density map after expansion of the best solution is shown in cyan contoured at 1σ and including data extrapolated to 1.7 Å. (b) Located anomalous substructure shown as green spheres derived from the S atoms of hellethionin D (NMR structure; PDB entry 1nbl; Milbradt et al., 2003 ▶), the resulting electron-density map after expansion, shown in blue contoured at 1σ and including data extrapolated to 1.0 Å, and the polyalanine trace of the solution obtained for viscotoxin A1 after the first fragment.
Figure 3
Figure 3
Structure solution with fragments with side chains. (a) Final structure of PRD2 shown as a backbone trace, with superimposed helices with side chains modelled in standard conformations, as located in the successful solution. (b) Detailed view of one of these helices superimposed on the final structure and the resulting electron-density map after SHELXE expansion contoured at 1σ and including data extrapolated to 1.7 Å. (c) Slightly misplaced polyalanine helix that nevertheless leads to structure solution in the case of viscotoxin A1. (d) Helix with cysteine side chain (yellow) in standard conformation used in the case of viscotoxin A1. In this case part of the helix is also misplaced, including the cysteine side chain, but this substructure also leads to a final electron-density map shown in cyan contoured at 1σ, including data extrapolated to 1.0 Å and characterized by a mean phase error of 18.9°. Figures were prepared with PyMOL and Coot (DeLano, 2002; Emsley et al., 2010 ▶).
Figure 4
Figure 4
Windows of the ARCIMBOLDO configuration GUI.
See this image and copyright information in PMC

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References

    1. Bieniossek, C., Schütz, P., Bumann, M., Limacher, A., Usón, I. & Baumann, U. (2006). J. Mol. Biol. 360, 457–465. - PubMed
    1. Caliandro, R., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Mazzone, A. & Siliqi, D. (2008). J. Appl. Cryst. 41, 548–553.
    1. Caliandro, R., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C. & Siliqi, D. (2005a). Acta Cryst. D61, 556–565. - PubMed
    1. Caliandro, R., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C. & Siliqi, D. (2005b). Acta Cryst. D61, 1080–1087. - PubMed
    1. DeLano, W. L. (2002). PyMOL http://www.pymol.org.

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