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Microcrystallography of Protein Crystals and In Cellulo Diffraction
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Protein phasing at non-atomic resolution by combining Patterson and VLD techniques.

Rocco Caliandro1, Benedetta Carrozzini1, Giovanni Luca Cascarano1

  • 1Istituto di Cristallografia, CNR, Via G. Amendola 122/O, 70126 Bari, Italy.

Acta Crystallographica. Section D, Biological Crystallography
|July 10, 2014
PubMed
Summary

Phasing proteins at resolutions down to 2.1 Å remains challenging. However, combining multiple algorithms in SIR2014 offers an efficient solution for protein structure determination and automatic model building.

Keywords:
Patterson techniquesVLDproteins

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein phasing at non-atomic resolution presents significant challenges for ab initio methods.
  • Overcoming the lack of experimental data requires advanced computational strategies.

Purpose of the Study:

  • To present a combined algorithmic approach for protein phasing at non-atomic resolution.
  • To demonstrate the feasibility and efficiency of this method for protein structure determination.

Main Methods:

  • Integration of diverse algorithms including Patterson deconvolution, superposition techniques, C map, VLD, FF function, SNIP, and free lunch extrapolation.
  • Application to protein diffraction data sets with resolutions down to 2.1 Å, requiring the presence of sulfur or heavier atoms.
  • Utilizing ARP/wARP for objective quality assessment of electron-density maps.

Main Results:

  • Resolution remains a primary obstacle in protein phasing.
  • The combined approach enables protein structure solution at 2.1 Å resolution, albeit exceptionally.
  • The method significantly improves efficiency, often yielding phases suitable for automatic model building.

Conclusions:

  • The integrated algorithm set in SIR2014 provides an efficient solution for protein phasing at lower resolutions.
  • This approach facilitates automatic model building, advancing structural biology.
  • Protein structure determination at 2.1 Å is feasible with this advanced computational strategy.