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Uniqueness and the ab initio phase problem in macromolecular crystallography.

D Baker1, A E Krukowski, D A Agard

  • 1Department of Biochemistry and Biophysics, The Howard Hughes Medical Institute, University of California, San Francisco, 94143-0448, USA.

Acta Crystallographica. Section D, Biological Crystallography
|January 1, 1993
PubMed
Summary

Solving the macromolecular crystallographic phase problem requires strong chemical constraints. Current methods using moderate resolution data and standard constraints yield multiple solutions, necessitating higher resolution data or improved constraints like macromolecular connectivity.

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Area of Science:

  • Crystallography
  • Structural Biology
  • Biophysics

Background:

  • The crystallographic phase problem is a critical challenge in determining macromolecular structures.
  • Ab initio approaches require sufficient chemical constraints to limit potential solutions.

Purpose of the Study:

  • To evaluate the effectiveness of common chemical constraints in solving the macromolecular phase problem.
  • To explore alternative or supplementary constraints for improving phase determination.

Main Methods:

  • Analysis of Fourier data sets at moderate resolution (2.5-3.0 Å).
  • Assessment of standard chemical constraints: positivity, atomicity, and solvent boundary.
  • Evaluation of entropy maximization as a phase determination method.
  • Development and application of a rapid algorithm for measuring macromolecular connectivity.

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Main Results:

  • Common chemical constraints are insufficient to uniquely solve the phase problem at moderate resolutions, leading to underdetermined solutions.
  • Entropy maximization can produce multiple false solutions with higher entropy than the correct one.
  • Macromolecular connectivity serves as a powerful constraint to reduce solution multiplicity.

Conclusions:

  • Successful ab initio macromolecular phasing necessitates high-resolution data and/or stronger chemical constraints.
  • Macromolecular connectivity is a valuable constraint for resolving ambiguities in the crystallographic phase problem.