Megahertz serial crystallography

Wiedorn, Max O.; Oberthür, Dominik; Bean, Richard; Schubert, Robin; Werner, N.; Abbey, Brian; Aepfelbacher, Martin; Adriano, Luigi; Allahgholi, A.; Al-Qudami, Nasser; Andreasson, Jakob; Aplin, S.; Awel, Salah; Ayyer, Kartik; Bajt, Saša; Barák, Imrich; Bari, Sadia; Bielecki, Johan; Botha, Sabine; Boukhelef, Djelloul; Brehm, Wolfgang; Brockhauser, Sándor; Cheviakov, Igor; Coleman, Matthew A.; Cruz-Mazo, Francisco; Danilevski, Cyril; Darmanin, Connie; Doak, R. Bruce; Domaracký, M.; Dörner, Katerina; Du, Yang; Fangohr, Hans; Fleckenstein, H.; Frank, Matthias; Fromme, Petra; Gañán‐Calvo, Alfonso M.; Gevorkov, Y.; Giewekemeyer, Klaus; Ginn, H.; Graafsma, H.; Graceffa, Rita; Greiffenberg, D.; Gumprecht, Lars; Göttlicher, P.; Hajdu, János; Hauf, Steffen; Heymann, Michaël; Holmes, Susannah; Horke, Daniel A.; Hunter, Mark S.; Imlau, Siegfried; Kaukher, A.; Kim, Yoonhee; Klyuev, A.; Knoška, J.; Kobe, Boštjan; Kuhn, Manuela; Kupitz, Christopher; Küpper, Jochen; Lahey-Rudolph, Janine Mia; Laurus, Torsten; Cong, K. Le; Letrun, Romain; Xavier, P. Lourdu; Maia, Luis; Maia, Filipe R. N. C.; Mariani, Valerio; Messerschmidt, Marc; Metz, Markus; Mezza, D.; Michelat, Thomas; Mills, Grant; Monteiro, Diana C. F.; Morgan, Andrew J.; Mühlig, Kerstin; Munke, Anna; Münnich, A.; Nette, Julia; Nugent, Keith A.; Nuguid, Theresa; Orville, Allen M.; Pandey, Suraj; Murillo, Gisel E. Peña; Villanueva-Pérez, P.; Poehlsen, J.; Previtali, Gianpietro; Redecke, Lars; Riekehr, Winnie Maria; Rohde, Holger; Round, Adam; Safenreiter, Tatiana; Sarrou, Iosifina; Sato, Tokushi; Schmidt, Marius; Schmitt, B.; Schönherr, Robert; Schulz, Joachim; Sellberg, Jonas A.; Seibert, M. Marvin; Seuring, Carolin; Shelby, Megan L.; Shoeman, Robert L.; Sikorski, Marcin; Silenzi, A.; Stan, Claudiu A.; Shi, X.; Stern, Stephan; Sztuk-Dambietz, Jola; Szuba, J.; Tolstikova, A.; Trebbin, Martin; Trunk, U.; Vagovič, Patrik; Ve, Thomas; Weinhausen, Britta; White, Thomas A.; Wrona, K.; Xu, Chen; Yefanov, Oleksandr; Zatsepin, Nadia A.; Zhang, Jiaguo; Perbandt, Markus; Mancuso, Adrian P.; Betzel, Christian; Chapman, Henry N.; Barty, Anton

doi:10.1038/s41467-018-06156-7

Cited by 178 publications

(131 citation statements)

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“…These explosions were admirably reported in detail by [8] from large series of experiments. The use of increasing frequencies of pulsation of XFELs up to the MHz range [9] to maximize the sample hit ratio has challenged the SFX practitioners. The damage caused to the samples upstream of the blast has been the subject of increasing attention [10].…”

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confidence: 99%

Scaling Laws of an Exploding Liquid Column under an Intense Ultrashort X-Ray Pulse

Gañán‐Calvo

2019

Phys. Rev. Lett.

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A general scaling of the evolution of an exploding liquid jet under an ultra short and intense X-ray pulse from a X-ray free electron laser (XFEL) is proposed. A general formulation of the conservation of energy for blasts in vacuum partially against a deformable object leads to a compact expression that governs the evolution of the gap produced by the explosion. The theoretical analysis contemplates two asymptotic stages for small and large times from the initiation of the blast. A complete dimensional analysis of the problem and an optimal collapse of experimental data reveal that the universal approximate analytical solution proposed is in remarkable agreement with experiments.The damage exerted by blasts in partial contact with deformable objects has been the subject of diverse studies of interest in mining [1], defense [2], or forensic applications [3, 4]. However, probably the strongest scientific interest in a detailed description of the damage caused by intense blasts has recently come with the advent of serial femtosecond crystallography (SFX) [5]. In this application, a microscopic jet produced by Flow Focusing [6,7] and loaded with protein crystal samples is exposed to focused femtosecond X-ray pulses from XFELs with energies in the range of mJ. As a consequence, the jet explodes in a vacuum chamber, generating a blast that splits the jet in two portions. These explosions were admirably reported in detail by [8] from large series of experiments. The use of increasing frequencies of pulsation of XFELs up to the MHz range [9] to maximize the sample hit ratio has challenged the SFX practitioners. The damage caused to the samples upstream of the blast has been the subject of increasing attention [10]. In this work we focus on the evolution of the blast [8] to precisely describe the physics of the process, obtaining the maximum expansion velocities and stresses undergone by the liquid column and the energies involved. To do that, we first propose a general formulation of the problem of blasts in vacuum, partially against deformable objects.General compact formulation of blasts in partial contact with deformable objects.-Consider a finite amount of condensed deformable matter M surrounded by vacuum. An amount of energy E D largely sufficient to vaporize a portion M g of that matter is suddenly injected in it. If part of M g is adjacent or in direct contact with the outer surface of M , it violently expands as a blast both into vacuum and against M (figure 1). The expanding hot gas domain V g (t) can be consider to comprise two virtual subdomains formally defined in the Supplemental Material: (i) V p (t), that pushes and deforms M by dominant pressure forces, and (ii) V e (t), whose mass and energy are constant by definition while it expands into vacuum. Therefore, V e (t) does not make any work on M . Those definitions and their implications do not impose any artificial condition on the natural evolution of the total gas domain V g (t). However, they provide a drastic simplification:as the initial energized ...

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confidence: 99%

Scaling Laws of an Exploding Liquid Column under an Intense Ultrashort X-Ray Pulse

Gañán‐Calvo

2019

Phys. Rev. Lett.

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“…Minimal-damage acquisition is ensured using a dose-fractionated diffraction-duringdestruction scheme and a-posteriori critical dose determination. We have demonstrated a net acquisition rate of 35 Hz when factoring in the hit fraction, which is comparable to current liquid-jet XFEL 8,9 and synchrotron fixed-target 11,12,18 experiments. Note that a further increase of more than an order of magnitude can be achieved if dose-fractionation is omitted and acquisition speed becomes detector frame rate limited.…”

Section: Discussionmentioning

confidence: 58%

Serial protein crystallography in an electron microscope

Bücker

Hogan-Lamarre

Mehrabi

et al. 2019

Preprint

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1 Sentence summary: Serial diffraction (SerialED) enables high-throughput, low dose protein crystallography from sub-micron crystals using conventional S/TEM microscopes. AbstractWe describe a new method for serial electron diffraction of protein nanocrystals using a conventional scanning/transmission electron microscope (S/TEM). Randomly dispersed crystals are mapped, and dose-efficient diffraction patterns measured at each identified crystal position for structure determination. Each crystal is measured in a single orientation without rotation. The automated workflow is suitable for high-throughput applications with acquisition rates of up to 1 kHz at a high hit fraction. A dose fractionation scheme allows for minimization of radiation damage effects and inherently optimal acquisition settings. We demonstrate this method by solving the structure of crystalline granulovirus occlusion bodies and lysozyme to a resolution of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid high-quality structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.We thank Djordje Gitaric for mechanical design work, Fabian Westermeier, David Pennicard, and Heinz Graafsma for adapting the Lambda detector for electron imaging, Anton Barty and Henry Chapman for many helpful discussions and critical reading of the manuscript, Thomas A. White for help with modifying CrystFEL for electron diffraction, and Michiel de Kock for help with image processing. We are indebted to Kay Grünewald and his research group for lending to us their cryo-transfer holder.

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“…Before that data can be merged, the full data set must be indexed. We used diffraction of beta-lactamase crystals from CXIDB ID 83 (Wiedorn et al, 2018) for comparison. This data set consists of a total of 14 445 patterns identified as containing crystal diffraction, which were indexed by a variety of algorithmsthe results are summarized in Tables 1 and 2 Comparison of the success rates of algorithms in indexing patterns as a function of the numbers of Bragg spots N in those patterns.…”

Section: Indexing Ratementioning

confidence: 99%

XGANDALF – extended gradient descent algorithm for lattice finding

Gevorkov

Yefanov

Barty

et al. 2019

Acta Crystallogr A Found Adv

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108

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Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real-time feedback during serial crystallography experiments. It is implemented in an open-source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.

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Megahertz serial crystallography

Cited by 178 publications

References 50 publications

Scaling Laws of an Exploding Liquid Column under an Intense Ultrashort X-Ray Pulse

Scaling Laws of an Exploding Liquid Column under an Intense Ultrashort X-Ray Pulse

Serial protein crystallography in an electron microscope

XGANDALF – extended gradient descent algorithm for lattice finding

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