Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data.

Journal Article (Journal Article)

Singular value decomposition (SVD) is a technique commonly used in the analysis of spectroscopic data that both acts as a noise filter and reduces the dimensionality of subsequent least-squares fits. To establish the applicability of SVD to crystallographic data, we applied SVD to calculated difference Fourier maps simulating those to be obtained in a time-resolved crystallographic study of photoactive yellow protein. The atomic structures of one dark state and three intermediates were used in qualitatively different kinetic mechanisms to generate time-dependent difference maps at specific time points. Random noise of varying levels in the difference structure factor amplitudes, different extents of reaction initiation, and different numbers of time points were all employed to simulate a range of realistic experimental conditions. Our results show that SVD allows for an unbiased differentiation between signal and noise; a small subset of singular values and vectors represents the signal well, reducing the random noise in the data. Due to this, phase information of the difference structure factors can be obtained. After identifying and fitting a kinetic mechanism, the time-independent structures of the intermediates could be recovered. This demonstrates that SVD will be a powerful tool in the analysis of experimental time-resolved crystallographic data.

Full Text

Duke Authors

Cited Authors

  • Schmidt, M; Rajagopal, S; Ren, Z; Moffat, K

Published Date

  • March 2003

Published In

Volume / Issue

  • 84 / 3

Start / End Page

  • 2112 - 2129

PubMed ID

  • 12609912

Pubmed Central ID

  • PMC1302779

International Standard Serial Number (ISSN)

  • 0006-3495

Digital Object Identifier (DOI)

  • 10.1016/S0006-3495(03)75018-8


  • eng

Conference Location

  • United States