Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching
Single-particle analysis (SPA) by X-ray free electron laser (XFEL) is a novel method that can observe biomolecules and living tissue that are difficult to crystallize in a state close to nature. To reconstruct three-dimensional (3D) molecular structure from two-dimensional (2D) XFEL diffraction patt...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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The Biophysical Society of Japan
2019-11-01
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| Series: | Biophysics and Physicobiology |
| Subjects: | |
| Online Access: | https://doi.org/10.2142/biophysico.16.0_367 |
| _version_ | 1818693599693373440 |
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| author | Miki Nakano Osamu Miyashita Florence Tama |
| author_facet | Miki Nakano Osamu Miyashita Florence Tama |
| author_sort | Miki Nakano |
| collection | DOAJ |
| description | Single-particle analysis (SPA) by X-ray free electron laser (XFEL) is a novel method that can observe biomolecules and living tissue that are difficult to crystallize in a state close to nature. To reconstruct three-dimensional (3D) molecular structure from two-dimensional (2D) XFEL diffraction patterns, we have to estimate the incident beam angle to the molecule for each pattern to assemble the 3D-diffraction intensity distribution using interpolation, and retrieve the phase information. In this study, we investigated the optimal parameter sets to assemble the 3D-diffraction intensity distribution from simulated 2D-diffraction patterns of ribosome. In particular, we examined how the parameters need to be adjusted for diffraction patterns with different binning sizes and beam intensities to obtain the highest resolution of molecular structure phase retrieved from the 3D-diffraction intensity. We found that resolution of restored molecular structure is sensitive to the interpolation parameters. Using the optimal parameter set, a linear oversampling ratio of around four is found to be sufficient for correct angle estimation and phase retrieval from the diffraction patterns of SPA by XFEL. |
| first_indexed | 2024-12-17T13:16:15Z |
| format | Article |
| id | doaj.art-f4da6200f6694a58b7bbfe8045c60f9c |
| institution | Directory Open Access Journal |
| issn | 2189-4779 |
| language | English |
| last_indexed | 2024-12-17T13:16:15Z |
| publishDate | 2019-11-01 |
| publisher | The Biophysical Society of Japan |
| record_format | Article |
| series | Biophysics and Physicobiology |
| spelling | doaj.art-f4da6200f6694a58b7bbfe8045c60f9c2022-12-21T21:47:00ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792019-11-011610.2142/biophysico.16.0_367Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matchingMiki Nakano0Osamu Miyashita1Florence Tama2RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, JapanRIKEN Center for Computational Science, Kobe, Hyogo 650-0047, JapanRIKEN Center for Computational Science, Kobe, Hyogo 650-0047, JapanSingle-particle analysis (SPA) by X-ray free electron laser (XFEL) is a novel method that can observe biomolecules and living tissue that are difficult to crystallize in a state close to nature. To reconstruct three-dimensional (3D) molecular structure from two-dimensional (2D) XFEL diffraction patterns, we have to estimate the incident beam angle to the molecule for each pattern to assemble the 3D-diffraction intensity distribution using interpolation, and retrieve the phase information. In this study, we investigated the optimal parameter sets to assemble the 3D-diffraction intensity distribution from simulated 2D-diffraction patterns of ribosome. In particular, we examined how the parameters need to be adjusted for diffraction patterns with different binning sizes and beam intensities to obtain the highest resolution of molecular structure phase retrieved from the 3D-diffraction intensity. We found that resolution of restored molecular structure is sensitive to the interpolation parameters. Using the optimal parameter set, a linear oversampling ratio of around four is found to be sufficient for correct angle estimation and phase retrieval from the diffraction patterns of SPA by XFEL.https://doi.org/10.2142/biophysico.16.0_367single-particle analysiscoherent x-ray diffraction imagingphase retrieval |
| spellingShingle | Miki Nakano Osamu Miyashita Florence Tama Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching Biophysics and Physicobiology single-particle analysis coherent x-ray diffraction imaging phase retrieval |
| title | Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching |
| title_full | Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching |
| title_fullStr | Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching |
| title_full_unstemmed | Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching |
| title_short | Parameter optimization for 3D-reconstruction from XFEL diffraction patterns based on Fourier slice matching |
| title_sort | parameter optimization for 3d reconstruction from xfel diffraction patterns based on fourier slice matching |
| topic | single-particle analysis coherent x-ray diffraction imaging phase retrieval |
| url | https://doi.org/10.2142/biophysico.16.0_367 |
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