Ab initio structure determination of a small protein, rubredoxin, by direct methods

Area of Science:

• Structural biology
• Computational chemistry
• X-ray crystallography

Background:

• Direct methods are crucial for solving the phase problem in X-ray crystallography.
• Accurate protein structure determination is vital for understanding biological function.
• Rubredoxin serves as a model system for validating new structure determination techniques.

Purpose of the Study:

• To evaluate the efficacy of the direct-methods program SAYTAN for protein structure solution.
• To assess the ability of SAYTAN to derive interpretable structural information from crystallographic data.
• To refine the determined rubredoxin structure using established crystallographic refinement software.

Main Methods:

• Application of the SAYTAN direct-methods program to rubredoxin crystallographic data.
• Utilizing multiple trials with random initial phases and selecting solutions by figures of merit.
• Employing phase extension and weighted Fourier recycling for structural model generation.
• Refinement of the structural model using SHELXL93 against 1 Å resolution data.

Main Results:

• SAYTAN successfully generated useful phase sets from random starting points.
• Phase extension and Fourier recycling revealed a recognizable rubredoxin structure.
• The final refined model achieved an R factor of 14.5% at 1 Å resolution.

Conclusions:

• The SAYTAN program is effective for solving protein structures using direct methods.
• The study validates the utility of SAYTAN in conjunction with phase extension and refinement techniques.
• High-resolution structural data of rubredoxin was obtained and refined, confirming the program's capability.