Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography
For direct phasing of protein crystals, a method based on the hybrid-input-output (HIO) algorithm has been proposed and tested on a variety of structures. So far, however, the diffraction data have been limited to high-resolution ones, i.e., higher than 2 Å. In principle, the methodology can be appl...
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| Format: | Article |
| Language: | English |
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MDPI AG
2018-04-01
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| Series: | Crystals |
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| Online Access: | http://www.mdpi.com/2073-4352/8/4/156 |
| _version_ | 1811184959873875968 |
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| author | Mengchao Jiang Hongxing He Yunpeng Cheng Wu-Pei Su |
| author_facet | Mengchao Jiang Hongxing He Yunpeng Cheng Wu-Pei Su |
| author_sort | Mengchao Jiang |
| collection | DOAJ |
| description | For direct phasing of protein crystals, a method based on the hybrid-input-output (HIO) algorithm has been proposed and tested on a variety of structures. So far, however, the diffraction data have been limited to high-resolution ones, i.e., higher than 2 Å. In principle, the methodology can be applied to data of lower resolutions, which might be particularly useful for phasing membrane protein crystals. For resolutions higher than 3.5 Å, it seems the atomic structure is solvable. For data of lower resolutions, information of the secondary structures and the protein boundary can still be obtained. Examples are given to support the conclusions. Real experimental data are used. Two aspects of the observed data have been discussed: removal of the measured low-resolution reflections and involvement of the unmeasured high-resolution reflections. The ab initio phasing employs histogram matching for density modification. A question arises whether the reference histogram used should match the resolution of the diffraction data or not. It seems that there is an optimal histogram which is good to use for data at various resolutions. |
| first_indexed | 2024-04-11T13:21:17Z |
| format | Article |
| id | doaj.art-43b94cb98439431e89440400fd7cef7d |
| institution | Directory Open Access Journal |
| issn | 2073-4352 |
| language | English |
| last_indexed | 2024-04-11T13:21:17Z |
| publishDate | 2018-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Crystals |
| spelling | doaj.art-43b94cb98439431e89440400fd7cef7d2022-12-22T04:22:11ZengMDPI AGCrystals2073-43522018-04-018415610.3390/cryst8040156cryst8040156Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray CrystallographyMengchao Jiang0Hongxing He1Yunpeng Cheng2Wu-Pei Su3Department of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204, USADepartment of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204, USADepartment of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204, USADepartment of Physics and Texas Center for Superconductivity, University of Houston, Houston, TX 77204, USAFor direct phasing of protein crystals, a method based on the hybrid-input-output (HIO) algorithm has been proposed and tested on a variety of structures. So far, however, the diffraction data have been limited to high-resolution ones, i.e., higher than 2 Å. In principle, the methodology can be applied to data of lower resolutions, which might be particularly useful for phasing membrane protein crystals. For resolutions higher than 3.5 Å, it seems the atomic structure is solvable. For data of lower resolutions, information of the secondary structures and the protein boundary can still be obtained. Examples are given to support the conclusions. Real experimental data are used. Two aspects of the observed data have been discussed: removal of the measured low-resolution reflections and involvement of the unmeasured high-resolution reflections. The ab initio phasing employs histogram matching for density modification. A question arises whether the reference histogram used should match the resolution of the diffraction data or not. It seems that there is an optimal histogram which is good to use for data at various resolutions.http://www.mdpi.com/2073-4352/8/4/156resolution dependencehybrid input-outputiterative projection algorithmab initio phasingmembrane proteinX-ray crystallography |
| spellingShingle | Mengchao Jiang Hongxing He Yunpeng Cheng Wu-Pei Su Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography Crystals resolution dependence hybrid input-output iterative projection algorithm ab initio phasing membrane protein X-ray crystallography |
| title | Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography |
| title_full | Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography |
| title_fullStr | Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography |
| title_full_unstemmed | Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography |
| title_short | Resolution Dependence of an Ab Initio Phasing Method in Protein X-ray Crystallography |
| title_sort | resolution dependence of an ab initio phasing method in protein x ray crystallography |
| topic | resolution dependence hybrid input-output iterative projection algorithm ab initio phasing membrane protein X-ray crystallography |
| url | http://www.mdpi.com/2073-4352/8/4/156 |
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