Applications Of The Hybrid Input-Output Method In Protein Crystallography

Date

2022-05

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Abstract

An iterative phasing method based on the hybrid input-output (HIO) algorithm is a promising method for solving the phase problem in protein crystallography. Two approaches for improving the iterative phasing method are proposed in this dissertation. During the phase retrieval, the iterative phasing method does not always succeed in the initial trial calculations. Even though there is no obvious sudden drop in the error metrics, there is still useful information in the results, such as the boundary information of the structure. Therefore, a two-step iterative phasing method with HIO is proposed. The first step is to determine a protein mask from the diffraction data with several thousand iterations. A good protein mask can be selected from the results with lower R values. The second step is to retrieve phases while keeping the pre-selected protein mask fixed. Two structures are solved successfully with the two-step iterative phasing method with HIO. The evolutions of the error metrics are presented, the final mean phase error is around 40. The calculated density map matches well with the deposited protein structure. Therefore, the failed results still contain useful information for further exploration. The iterative phasing method can incorporate partial structures to solve structures with low solvent content. Trial calculations are presented, assuming one of the chains is known. In each iteration, the calculated densities in the known region are set to the densities of the known partial structure. Most calculations retrieve the phases successfully.

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Keywords

Hybrid input-output, Crystallography, Protein

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