Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser
Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to c...
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
International Union of Crystallography
2021-11-01
|
| Series: | IUCrJ |
| Subjects: | |
| Online Access: | http://scripts.iucr.org/cgi-bin/paper?S2052252521008046 |
| _version_ | 1818320301814972416 |
|---|---|
| author | Karol Nass Camila Bacellar Claudio Cirelli Florian Dworkowski Yaroslav Gevorkov Daniel James Philip J. M. Johnson Demet Kekilli Gregor Knopp Isabelle Martiel Dmitry Ozerov Alexandra Tolstikova Laura Vera Tobias Weinert Oleksandr Yefanov Jörg Standfuss Sven Reiche Christopher J. Milne |
| author_facet | Karol Nass Camila Bacellar Claudio Cirelli Florian Dworkowski Yaroslav Gevorkov Daniel James Philip J. M. Johnson Demet Kekilli Gregor Knopp Isabelle Martiel Dmitry Ozerov Alexandra Tolstikova Laura Vera Tobias Weinert Oleksandr Yefanov Jörg Standfuss Sven Reiche Christopher J. Milne |
| author_sort | Karol Nass |
| collection | DOAJ |
| description | Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [Δλ/λ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs. |
| first_indexed | 2024-12-13T10:22:50Z |
| format | Article |
| id | doaj.art-ad50bebd17b6464fb70fffcb3373aa32 |
| institution | Directory Open Access Journal |
| issn | 2052-2525 |
| language | English |
| last_indexed | 2024-12-13T10:22:50Z |
| publishDate | 2021-11-01 |
| publisher | International Union of Crystallography |
| record_format | Article |
| series | IUCrJ |
| spelling | doaj.art-ad50bebd17b6464fb70fffcb3373aa322022-12-21T23:51:08ZengInternational Union of CrystallographyIUCrJ2052-25252021-11-018690592010.1107/S2052252521008046zf5018Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laserKarol Nass0Camila Bacellar1Claudio Cirelli2Florian Dworkowski3Yaroslav Gevorkov4Daniel James5Philip J. M. Johnson6Demet Kekilli7Gregor Knopp8Isabelle Martiel9Dmitry Ozerov10Alexandra Tolstikova11Laura Vera12Tobias Weinert13Oleksandr Yefanov14Jörg Standfuss15Sven Reiche16Christopher J. Milne17Paul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandCenter for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, GermanyPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandCenter for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, GermanyPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandCenter for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg 22607, GermanyPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandPaul Scherrer Institut, Forschungstrasse 111, Villigen 5232, SwitzerlandSerial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [Δλ/λ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (Δλ/λ = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs.http://scripts.iucr.org/cgi-bin/paper?S2052252521008046pink beamsserial femtosecond crystallographyde novo protein structure determinationsingle-wavelength anomalous diffractionxfelslarge bandwidthsdata-quality indicators |
| spellingShingle | Karol Nass Camila Bacellar Claudio Cirelli Florian Dworkowski Yaroslav Gevorkov Daniel James Philip J. M. Johnson Demet Kekilli Gregor Knopp Isabelle Martiel Dmitry Ozerov Alexandra Tolstikova Laura Vera Tobias Weinert Oleksandr Yefanov Jörg Standfuss Sven Reiche Christopher J. Milne Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser IUCrJ pink beams serial femtosecond crystallography de novo protein structure determination single-wavelength anomalous diffraction xfels large bandwidths data-quality indicators |
| title | Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser |
| title_full | Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser |
| title_fullStr | Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser |
| title_full_unstemmed | Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser |
| title_short | Pink-beam serial femtosecond crystallography for accurate structure-factor determination at an X-ray free-electron laser |
| title_sort | pink beam serial femtosecond crystallography for accurate structure factor determination at an x ray free electron laser |
| topic | pink beams serial femtosecond crystallography de novo protein structure determination single-wavelength anomalous diffraction xfels large bandwidths data-quality indicators |
| url | http://scripts.iucr.org/cgi-bin/paper?S2052252521008046 |
| work_keys_str_mv | AT karolnass pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT camilabacellar pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT claudiocirelli pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT floriandworkowski pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT yaroslavgevorkov pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT danieljames pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT philipjmjohnson pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT demetkekilli pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT gregorknopp pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT isabellemartiel pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT dmitryozerov pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT alexandratolstikova pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT lauravera pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT tobiasweinert pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT oleksandryefanov pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT jorgstandfuss pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT svenreiche pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser AT christopherjmilne pinkbeamserialfemtosecondcrystallographyforaccuratestructurefactordeterminationatanxrayfreeelectronlaser |