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Single-molecule imaging with longer X-ray laser pulses.

Martin AV, Corso JK, Caleman C, Timneanu N, Quiney HM - IUCrJ (2015)

Bottom Line: One of the key reasons for this success is the 'self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes.As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5-10 fs, but can succeed for pulses 50-100 fs in duration.The results suggest that sub-nanometre single-molecule imaging with 30-50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out.

View Article: PubMed Central - HTML - PubMed

Affiliation: ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia.

ABSTRACT
During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the 'self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5-10 fs, but can succeed for pulses 50-100 fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage ('damage noise'). The results suggest that sub-nanometre single-molecule imaging with 30-50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.

No MeSH data available.


Related in: MedlinePlus

The effects of damage on the atomic structure factor. The term f0(q) is the undamaged atomic scattering factor for an unionized C atom, A(q) is proportional to the mean intensity per C atom at each resolution shell, B(q) is proportional to the speckle contrast for carbon and σB(q) is the standard deviation of the shot-to-shot fluctuations of the speckle due to damage. When there is no damage, A(q) and B(q) are equal to . The simulation parameters were 8 keV photon energy, 40 fs pulse duration, 2 mJ pulse energy and spot size of 100 × 100 nm.
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fig2: The effects of damage on the atomic structure factor. The term f0(q) is the undamaged atomic scattering factor for an unionized C atom, A(q) is proportional to the mean intensity per C atom at each resolution shell, B(q) is proportional to the speckle contrast for carbon and σB(q) is the standard deviation of the shot-to-shot fluctuations of the speckle due to damage. When there is no damage, A(q) and B(q) are equal to . The simulation parameters were 8 keV photon energy, 40 fs pulse duration, 2 mJ pulse energy and spot size of 100 × 100 nm.

Mentions: Simulations were performed at a photon energy of 8 keV (wavelength ∼0.155 nm), which is sufficient resolution for structural biology and similar to that demonstrated in simulation studies of single-molecule imaging (Tegze & Bortel, 2012 ▸). The principal effects of damage on molecular diffraction can be seen in Fig. 2 ▸, which shows a simulation for a pulse duration of 40 fs, a beam intensity of 5 × 1020 W cm−2 (corresponding to a 2 mJ pulse) and a spot size of 100 × 100 nm2. As the energy bandwidth of an XFEL is typically around 0.2%, we expect it to have no significant impact on damage. Without damage A(q) would be equal to , but with damage it is reduced, attenuating the mean intensity by the same amount. The attenuation occurs at all resolutions, but is a greater fraction of the original signal at lower resolutions. As shown in a recent damage study (Caleman et al., 2015 ▸), this effect is due to valence-shell ionization, because the scattering factors of valence electrons scatter at lower angles compared with core–shell ionization or ion diffusion. Ion diffusion attenuates preferentially at higher resolution before lower resolution, and core–shell ionization attenuates both high and low resolution at similar rates. The term B(q) is lower than A(q) because of the effects of ion motion and the discrepancy is more pronounced at higher resolution. At 40 fs, the root mean-square (r.m.s.) displacement of ions due to diffusion is around 11 Å for H, less than 0.1 Å for S and 0.2–0.4 Å for C, N and O. This indicates that ion diffusion is not a dominant process under these pulse conditions for the non-H atoms that contribute the bulk of the scattering. The deviations between A(q) and B(q) are important for accurate structure retrieval methods (Quiney & Nugent, 2011 ▸). In this case, the most significant damage noise term σB(q) is lower than B(q) across all resolutions, indicating that, even for pulse durations as long as 40 fs, damage noise does not exceed the signal from the average molecular structure.


Single-molecule imaging with longer X-ray laser pulses.

Martin AV, Corso JK, Caleman C, Timneanu N, Quiney HM - IUCrJ (2015)

The effects of damage on the atomic structure factor. The term f0(q) is the undamaged atomic scattering factor for an unionized C atom, A(q) is proportional to the mean intensity per C atom at each resolution shell, B(q) is proportional to the speckle contrast for carbon and σB(q) is the standard deviation of the shot-to-shot fluctuations of the speckle due to damage. When there is no damage, A(q) and B(q) are equal to . The simulation parameters were 8 keV photon energy, 40 fs pulse duration, 2 mJ pulse energy and spot size of 100 × 100 nm.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4645111&req=5

fig2: The effects of damage on the atomic structure factor. The term f0(q) is the undamaged atomic scattering factor for an unionized C atom, A(q) is proportional to the mean intensity per C atom at each resolution shell, B(q) is proportional to the speckle contrast for carbon and σB(q) is the standard deviation of the shot-to-shot fluctuations of the speckle due to damage. When there is no damage, A(q) and B(q) are equal to . The simulation parameters were 8 keV photon energy, 40 fs pulse duration, 2 mJ pulse energy and spot size of 100 × 100 nm.
Mentions: Simulations were performed at a photon energy of 8 keV (wavelength ∼0.155 nm), which is sufficient resolution for structural biology and similar to that demonstrated in simulation studies of single-molecule imaging (Tegze & Bortel, 2012 ▸). The principal effects of damage on molecular diffraction can be seen in Fig. 2 ▸, which shows a simulation for a pulse duration of 40 fs, a beam intensity of 5 × 1020 W cm−2 (corresponding to a 2 mJ pulse) and a spot size of 100 × 100 nm2. As the energy bandwidth of an XFEL is typically around 0.2%, we expect it to have no significant impact on damage. Without damage A(q) would be equal to , but with damage it is reduced, attenuating the mean intensity by the same amount. The attenuation occurs at all resolutions, but is a greater fraction of the original signal at lower resolutions. As shown in a recent damage study (Caleman et al., 2015 ▸), this effect is due to valence-shell ionization, because the scattering factors of valence electrons scatter at lower angles compared with core–shell ionization or ion diffusion. Ion diffusion attenuates preferentially at higher resolution before lower resolution, and core–shell ionization attenuates both high and low resolution at similar rates. The term B(q) is lower than A(q) because of the effects of ion motion and the discrepancy is more pronounced at higher resolution. At 40 fs, the root mean-square (r.m.s.) displacement of ions due to diffusion is around 11 Å for H, less than 0.1 Å for S and 0.2–0.4 Å for C, N and O. This indicates that ion diffusion is not a dominant process under these pulse conditions for the non-H atoms that contribute the bulk of the scattering. The deviations between A(q) and B(q) are important for accurate structure retrieval methods (Quiney & Nugent, 2011 ▸). In this case, the most significant damage noise term σB(q) is lower than B(q) across all resolutions, indicating that, even for pulse durations as long as 40 fs, damage noise does not exceed the signal from the average molecular structure.

Bottom Line: One of the key reasons for this success is the 'self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes.As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5-10 fs, but can succeed for pulses 50-100 fs in duration.The results suggest that sub-nanometre single-molecule imaging with 30-50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out.

View Article: PubMed Central - HTML - PubMed

Affiliation: ARC Centre of Excellence for Advanced Molecular Imaging, School of Physics, University of Melbourne, Parkville, Victoria 3010, Australia.

ABSTRACT
During the last five years, serial femtosecond crystallography using X-ray laser pulses has been developed into a powerful technique for determining the atomic structures of protein molecules from micrometre- and sub-micrometre-sized crystals. One of the key reasons for this success is the 'self-gating' pulse effect, whereby the X-ray laser pulses do not need to outrun all radiation damage processes. Instead, X-ray-induced damage terminates the Bragg diffraction prior to the pulse completing its passage through the sample, as if the Bragg diffraction were generated by a shorter pulse of equal intensity. As a result, serial femtosecond crystallography does not need to be performed with pulses as short as 5-10 fs, but can succeed for pulses 50-100 fs in duration. It is shown here that a similar gating effect applies to single-molecule diffraction with respect to spatially uncorrelated damage processes like ionization and ion diffusion. The effect is clearly seen in calculations of the diffraction contrast, by calculating the diffraction of the average structure separately to the diffraction from statistical fluctuations of the structure due to damage ('damage noise'). The results suggest that sub-nanometre single-molecule imaging with 30-50 fs pulses, like those produced at currently operating facilities, should not yet be ruled out. The theory presented opens up new experimental avenues to measure the impact of damage on single-particle diffraction, which is needed to test damage models and to identify optimal imaging conditions.

No MeSH data available.


Related in: MedlinePlus