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SAD phasing by OASIS-2004: case studies of dual-space fragment extension

De-qiang Yao1, Sheng Huang, Jia-wei Wang

  • 1Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100080, People's Republic of China.

Acta Crystallographica. Section D, Biological Crystallography
|July 21, 2006
PubMed

Insights

This study introduces an iterative dual-space phasing method using four programs to improve automated protein structure determination from single-wavelength anomalous diffraction (SAD) data, enhancing high-throughput capabilities.

Area of Science:

  • Structural Biology
  • X-ray Crystallography
  • Biophysics

Background:

  • Single-wavelength anomalous diffraction (SAD) is a crucial technique for protein structure determination.
  • Phase ambiguity is a significant challenge in SAD experiments, hindering automated model building.

Purpose of the Study:

  • To develop and evaluate an iterative dual-space phasing procedure for improving automated protein model building using SAD data.
  • To assess the contributions of individual software packages within the workflow.

Main Methods:

  • Iterative dual-space fragment extension incorporating known anomalous scatterers and partial protein models.
  • Utilizing OASIS-2004 for initial phase ambiguity resolution.
  • Employing DM for phase improvement via density modification.
  • Using RESOLVE for initial model building and ARP/wARP for structure completion.

Main Results:

  • The developed procedure successfully addressed phase ambiguity in SAD data.
  • Iterative refinement using dual-space phasing significantly improved automated model building.
  • Case studies with challenging SAD datasets demonstrated the method's effectiveness.

Conclusions:

  • The four-program workflow, based on iterative dual-space phasing, is beneficial for high-throughput protein structure determination.
  • Each program (OASIS-2004, DM, RESOLVE, ARP/wARP) plays a distinct and vital role in the process.

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