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Automated MAD and MIR structure solution.

Terwilliger TC, Berendzen J - Acta Crystallogr. D Biol. Crystallogr. (1999)

Bottom Line: These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation.The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit.The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

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Affiliation: Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

ABSTRACT
Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

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Steps in automated structure determination by SOLVE.
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fig1: Steps in automated structure determination by SOLVE.

Mentions: Fig. 1 ▶ outlines the main steps carried out by the automated ‘SOLVE’ procedure for MIR and MAD structure determination. These consist of scaling the data, calculation of Patterson functions, finding and optimizing the heavy-atom partial structure and calculating native phases and an electron-density map. The procedures for MAD and MIR data are very similar, except that the MAD data is scaled slightly differently from MIR data and the MAD data is converted to a pseudo-SIRAS (single isomorphous replacement with anomalous scattering) form before looking for the anomalously scattering-atom partial structure. This conversion allows heavy-atom refinement, which would otherwise be prohibitively slow, to be carried out very quickly by Patterson-based refinement (Terwilliger & Eisenberg, 1983 ▶; Terwilliger, 1994b ▶). Each of these steps is described in detail below.


Automated MAD and MIR structure solution.

Terwilliger TC, Berendzen J - Acta Crystallogr. D Biol. Crystallogr. (1999)

Steps in automated structure determination by SOLVE.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2746121&req=5

fig1: Steps in automated structure determination by SOLVE.
Mentions: Fig. 1 ▶ outlines the main steps carried out by the automated ‘SOLVE’ procedure for MIR and MAD structure determination. These consist of scaling the data, calculation of Patterson functions, finding and optimizing the heavy-atom partial structure and calculating native phases and an electron-density map. The procedures for MAD and MIR data are very similar, except that the MAD data is scaled slightly differently from MIR data and the MAD data is converted to a pseudo-SIRAS (single isomorphous replacement with anomalous scattering) form before looking for the anomalously scattering-atom partial structure. This conversion allows heavy-atom refinement, which would otherwise be prohibitively slow, to be carried out very quickly by Patterson-based refinement (Terwilliger & Eisenberg, 1983 ▶; Terwilliger, 1994b ▶). Each of these steps is described in detail below.

Bottom Line: These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation.The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit.The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

ABSTRACT
Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations.

Show MeSH
Related in: MedlinePlus