In-house sulfur SAD phasing: a case study of the effects of data quality and resolution cutoffs

Acta Crystallogr D Biol Crystallogr. 2006 Jul;62(Pt 7):707-16. doi: 10.1107/S0907444906014946. Epub 2006 Jun 20.

Abstract

Single-wavelength anomalous diffraction (SAD) utilizing the weak signal of inherently present S atoms can be successfully used to solve macromolecular structures, although this is mostly performed with data from a synchrotron rather than a laboratory source. Using high redundancy, sufficiently accurate anomalous data may now often be collected in the laboratory using Cu Kalpha X-ray radiation. Systematic analyses of a laboratory-derived data set illuminate the effects of data quality, redundancy and resolution cutoffs on the ability to locate the S atoms and phase the structure of Ptr ToxA, a 13.2 kDa toxin secreted by the fungus Pyrenophora tritici-repentis. Three sulfurs contributed to the successful phasing of the structure and were located using the program SHELXD. It is observed that data quality improves with increasing redundancy, but after a certain point becomes worse owing to crystal decay, so that there is an optimal amount of data to include for the sulfur substructure solution. Further, the success rate in locating S atoms is dramatically improved at lower resolutions and in a manner similar to data quality, there exists an optimal resolution at which the likelihood of solving the substructure is maximized. Based on these observations, a strategy for SAD data collection and substructure solution is suggested.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Crystallization
  • Crystallography, X-Ray / methods*
  • Fungal Proteins / chemistry*
  • Models, Molecular
  • Mycotoxins / chemistry*
  • Protein Conformation
  • Scattering, Radiation
  • Sulfur / chemistry*

Substances

  • Fungal Proteins
  • Mycotoxins
  • TOXA protein, Pyrenophora tritici-repentis
  • Sulfur