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Valerio
Bellucci
,
Sarlota
Birnsteinova
,
Tokushi
Sato
,
Romain
Letrun
,
Jayanath C. P.
Koliyadu
,
Chan
Kim
,
Gabriele
Giovanetti
,
Carsten
Deiter
,
Liubov
Samoylova
,
Ilia
Petrov
,
Luis
Lopez Morillo
,
Rita
Graceffa
,
Luigi
Adriano
,
Helge
Huelsen
,
Heiko
Kollmann
,
Thu Nhi
Tran Calliste
,
Dusan
Korytar
,
Zdenko
Zaprazny
,
Andrea
Mazzolari
,
Marco
Romagnoni
,
Eleni Myrto
Asimakopoulou
,
Zisheng
Yao
,
Yuhe
Zhang
,
Jozef
Ulicny
,
Alke
Meents
,
Henry N.
Chapman
,
Richard
Bean
,
Adrian
Mancuso
,
Pablo
Villanueva-Perez
,
Patrik
Vagovic
Open Access
Abstract: X-ray multi-projection imaging (XMPI) is an emerging experimental technique for the acquisition of rotation-free, time-resolved, volumetric information on stochastic processes. The technique is developed for high-brilliance light-source facilities, aiming to address known limitations of state-of-the-art imaging methods in the acquisition of 4D sample information, linked to their need for sample rotation. XMPI relies on a beam-splitting scheme, that illuminates a sample from multiple, angularly spaced viewpoints, and employs fast, indirect, X-ray imaging detectors for the collection of the data. This approach enables studies of previously inaccessible phenomena of industrial and societal relevance such as fractures in solids, propagation of shock waves, laser-based 3D printing, or even fast processes in the biological domain. In this work, we discuss in detail the beam-splitting scheme of XMPI. More specifically, we explore the relevant properties of X-ray splitter optics for their use in XMPI schemes, both at synchrotron insertion devices and XFEL facilities. Furthermore, we describe two distinct XMPI schemes, designed to faciliate large samples and complex sample environments. Finally, we present experimental proof of the feasibility of MHz-rate XMPI at the European XFEL. This detailed overview aims to state the challenges and the potential of XMPI and act as a stepping stone for future development of the technique.
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Nov 2024
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Jayanath C. P.
Koliyadu
,
Daniel
Moško
,
Eleni Myrto
Asimakopoulou
,
Valerio
Bellucci
,
Šarlota
Birnšteinová
,
Richard
Bean
,
Romain
Letrun
,
Chan
Kim
,
Henry
Kirkwood
,
Gabriele
Giovanetti
,
Nerea
Jardon
,
Janusz
Szuba
,
Trey
Guest
,
Andreas
Koch
,
Jan
Grünert
,
Peter
Szeles
,
Pablo
Villanueva-Perez
,
Fabian
Reuter
,
Claus-Dieter
Ohl
,
Mike Andreas
Noack
,
Francisco
Garcia-Moreno
,
Zuzana
Kuglerová-Valdová
,
Libor
Juha
,
Martin
Nikl
,
Wataru
Yashiro
,
Hitoshi
Soyama
,
Daniel
Eakins
,
Alexander M.
Korsunsky
,
Jozef
Ulicny
,
Alke
Meents
,
Henry N.
Chapman
,
Adrian P.
Mancuso
,
Tokushi
Sato
,
Patrik
Vagovic
Abstract: We report on recent developments that enable megahertz hard X-ray phase contrast imaging (MHz XPCI) experiments at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of the European XFEL facility (EuXFEL). We describe the technical implementation of the key components, including an MHz fast camera and a modular indirect X-ray microscope system based on fast scintillators coupled through a high-resolution optical microscope, which enable full-field X-ray microscopy with phase contrast of fast and irreversible phenomena. The image quality for MHz XPCI data showed significant improvement compared with a pilot demonstration of the technique using parallel beam illumination, which also allows access to up to 24 keV photon energies at the SPB/SFX instrument of the EuXFEL. With these developments, MHz XPCI was implemented as a new method offered for a broad user community (academic and industrial) and is accessible via standard user proposals. Furthermore, intra-train pulse diagnostics with a high few-micrometre spatial resolution and recording up to 128 images of consecutive pulses in a train at up to 1.1 MHz repetition rate is available upstream of the instrument. Together with the diagnostic camera upstream of the instrument and the MHz XPCI setup at the SPB/SFX instrument, simultaneous two-plane measurements for future beam studies and feedback for machine parameter tuning are now possible.
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Nov 2024
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Zhou
Shen
,
Paul Lourdu
Xavier
,
Richard
Bean
,
Johan
Bielecki
,
Martin
Bergemann
,
Benedikt
Daurer
,
Tomas
Ekeberg
,
Armando D.
Estillore
,
Hans
Fangohr
,
Klaus
Giewekemeyer
,
Mikhail
Karnevskiy
,
Richard A.
Kirian
,
Henry
Kirkwood
,
Yoonhee
Kim
,
Jayanath C. P.
Koliyadu
,
Holger
Lange
,
Romain
Letrun
,
Jannik
Lübke
,
Abhishek
Mall
,
Thomas
Michelat
,
Andrew J.
Morgan
,
Nils
Roth
,
Amit K.
Samanta
,
Tokushi
Sato
,
Marcin
Sikorski
,
Florian
Schulz
,
Patrik
Vagovic
,
Tamme
Wollweber
,
Lena
Worbs
,
Filipe
Maia
,
Daniel A.
Horke
,
Jochen
Küpper
,
Adrian P.
Mancuso
,
Henry
Chapman
,
Kartik
Ayyer
,
N. Duane
Loh
Open Access
Abstract: Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with X-ray free-electron lasers (XFELs) creates opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between 105 structural models and 106 XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the nonequilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable “shape envelope” among nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles’ shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.
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May 2024
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Tomas
Ekeberg
,
Dameli
Assalauova
,
Johan
Bielecki
,
Rebecca
Boll
,
Benedikt J.
Daurer
,
Lutz A.
Eichacker
,
Linda E.
Franken
,
Davide E.
Galli
,
Luca
Gelisio
,
Lars
Gumprecht
,
Laura H.
Gunn
,
Janos
Hajdu
,
Robert
Hartmann
,
Dirk
Hasse
,
Alexandr
Ignatenko
,
Jayanath
Koliyadu
,
Olena
Kulyk
,
Ruslan
Kurta
,
Markus
Kuster
,
Wolfgang
Lugmayr
,
Jannik
Lübke
,
Adrian P.
Mancuso
,
Tommaso
Mazza
,
Carl
Nettelblad
,
Yevheniy
Ovcharenko
,
Daniel E.
Rivas
,
Max
Rose
,
Amit K.
Samanta
,
Philipp
Schmidt
,
Egor
Sobolev
,
Nicusor
Timneanu
,
Sergey
Usenko
,
Daniel
Westphal
,
Tamme
Wollweber
,
Lena
Worbs
,
Paul Lourdu
Xavier
,
Hazem
Yousef
,
Kartik
Ayyer
,
Henry N.
Chapman
,
Jonas A.
Sellberg
,
Carolin
Seuring
,
Ivan A.
Vartanyants
,
Jochen
Küpper
,
Michael
Meyer
,
Filipe R. N. C.
Maia
Open Access
Abstract: The idea of using ultrashort X-ray pulses to obtain images of single proteins frozen in time has fascinated and inspired many. It was one of the arguments for building X-ray free-electron lasers. According to theory, the extremely intense pulses provide sufficient signal to dispense with using crystals as an amplifier, and the ultrashort pulse duration permits capturing the diffraction data before the sample inevitably explodes. This was first demonstrated on biological samples a decade ago on the giant mimivirus. Since then, a large collaboration has been pushing the limit of the smallest sample that can be imaged. The ability to capture snapshots on the timescale of atomic vibrations, while keeping the sample at room temperature, may allow probing the entire conformational phase space of macromolecules. Here we show the first observation of an X-ray diffraction pattern from a single protein, that of Escherichia coli GroEL which at 14 nm in diameter is the smallest biological sample ever imaged by X-rays, and demonstrate that the concept of diffraction before destruction extends to single proteins. From the pattern, it is possible to determine the approximate orientation of the protein. Our experiment demonstrates the feasibility of ultrafast imaging of single proteins, opening the way to single-molecule time-resolved studies on the femtosecond timescale.
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Jan 2024
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Sarlota
Birnsteinova
,
Danilo E.
Ferreira De Lima
,
Egor
Sobolev
,
Henry J.
Kirkwood
,
Valerio
Bellucci
,
Richard J.
Bean
,
Chan
Kim
,
Jayanath C. P.
Koliyadu
,
Tokushi
Sato
,
Fabio
Dall'Antonia
,
Eleni Myrto
Asimakopoulou
,
Zisheng
Yao
,
Khachiwan
Buakor
,
Yuhe
Zhang
,
Alke
Meents
,
Henry N.
Chapman
,
Adrian P.
Mancuso
,
Pablo
Villanueva-Perez
,
Patrik
Vagovic
Open Access
Abstract: The high pulse intensity and repetition rate of the European X-ray Free-Electron Laser (EuXFEL) provide superior temporal resolution compared with other X-ray sources. In combination with MHz X-ray microscopy techniques, it offers a unique opportunity to achieve superior contrast and spatial resolution in applications demanding high temporal resolution. In both live visualization and offline data analysis for microscopy experiments, baseline normalization is essential for further processing steps such as phase retrieval and modal decomposition. In addition, access to normalized projections during data acquisition can play an important role in decision-making and improve the quality of the data. However, the stochastic nature of X-ray free-electron laser sources hinders the use of standard flat-field normalization methods during MHz X-ray microscopy experiments. Here, an online (i.e. near real-time) dynamic flat-field correction method based on principal component analysis of dynamically evolving flat-field images is presented. The method is used for the normalization of individual X-ray projections and has been implemented as a near real-time analysis tool at the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument of EuXFEL.
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Nov 2023
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I13-1-Coherence
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Valerio
Bellucci
,
Marie-Christine
Zdora
,
Ladislav
Mikes
,
Šarlota
Birnšteinová
,
Peter
Oberta
,
Marco
Romagnoni
,
Andrea
Mazzolari
,
Pablo
Villanueva-Perez
,
Rajmund
Mokso
,
Christian
David
,
Mikako
Makita
,
Silvia
Cipiccia
,
Jozef
Ulicny
,
Alke
Meents
,
Adrian P.
Mancuso
,
Henry N.
Chapman
,
Patrik
Vagovic
Diamond Proposal Number(s):
[17739]
Open Access
Abstract: The characterisation of fast phenomena at the microscopic scale is required for the understanding of catastrophic responses of materials to loads and shocks, the processing of materials by optical or mechanical means, the processes involved in many key technologies such as additive manufacturing and microfluidics, and the mixing of fuels in combustion. Such processes are usually stochastic in nature and occur within the opaque interior volumes of materials or samples, with complex dynamics that evolve in all three dimensions at speeds exceeding many meters per second. There is therefore a need for the ability to record three-dimensional X-ray movies of irreversible processes with resolutions of micrometers and frame rates of microseconds. Here we demonstrate a method to achieve this by recording a stereo phase-contrast image pair in a single exposure. The two images are combined computationally to reconstruct a 3D model of the object. The method is extendable to more than two simultaneous views. When combined with megahertz pulse trains of X-ray free-electron lasers (XFELs) it will be possible to create movies able to resolve 3D trajectories with velocities of kilometers per second.
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May 2023
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Vasundara
Srinivasan
,
Hévila
Brognaro
,
Prince R.
Prabhu
,
Edmarcia Elisa
De Souza
,
Sebastian
Günther
,
Patrick Y. A.
Reinke
,
Thomas J.
Lane
,
Helen
Ginn
,
Huijong
Han
,
Wiebke
Ewert
,
Janina
Sprenger
,
Faisal H. M.
Koua
,
Sven
Falke
,
Nadine
Werner
,
Hina
Andaleeb
,
Najeeb
Ullah
,
Bruno Alves
Franca
,
Mengying
Wang
,
Angélica Luana C.
Barra
,
Markus
Perbandt
,
Martin
Schwinzer
,
Christina
Schmidt
,
Lea
Brings
,
Kristina
Lorenzen
,
Robin
Schubert
,
Rafael Rahal Guaragna
Machado
,
Erika Donizette
Candido
,
Danielle Bruna Leal
Oliveira
,
Edison Luiz
Durigon
,
Stephan
Niebling
,
Angelica
Struve Garcia
,
Oleksandr
Yefanov
,
Julia
Lieske
,
Luca
Gelisio
,
Martin
Domaracky
,
Philipp
Middendorf
,
Michael
Groessler
,
Fabian
Trost
,
Marina
Galchenkova
,
Aida Rahmani
Mashhour
,
Sofiane
Saouane
,
Johanna
Hakanpää
,
Markus
Wolf
,
Maria
Garcia Alai
,
Dusan
Turk
,
Arwen R.
Pearson
,
Henry N.
Chapman
,
Winfried
Hinrichs
,
Carsten
Wrenger
,
Alke
Meents
,
Christian
Betzel
Open Access
Abstract: SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host’s innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.
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Aug 2022
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Sebastian
Gunther
,
Patrick Y. A.
Reinke
,
Yaiza
Fernández-García
,
Julia
Lieske
,
Thomas J.
Lane
,
Helen M.
Ginn
,
Faisal H. M.
Koua
,
Christiane
Ehrt
,
Wiebke
Ewert
,
Dominik
Oberthuer
,
Oleksandr
Yefanov
,
Susanne
Meier
,
Kristina
Lorenzen
,
Boris
Krichel
,
Janine-Denise
Kopicki
,
Luca
Gelisio
,
Wolfgang
Brehm
,
Ilona
Dunkel
,
Brandon
Seychell
,
Henry
Gieseler
,
Brenna
Norton-Baker
,
Beatriz
Escudero-Pérez
,
Martin
Domaracky
,
Sofiane
Saouane
,
Alexandra
Tolstikova
,
Thomas A.
White
,
Anna
Hänle
,
Michael
Groessler
,
Holger
Fleckenstein
,
Fabian
Trost
,
Marina
Galchenkova
,
Yaroslav
Gevorkov
,
Chufeng
Li
,
Salah
Awel
,
Ariana
Peck
,
Miriam
Barthelmess
,
Frank
Schluenzen
,
Paulraj
Lourdu Xavier
,
Nadine
Werner
,
Hina
Andaleeb
,
Najeeb
Ullah
,
Sven
Falke
,
Vasundara
Srinivasan
,
Bruno Alves
França
,
Martin
Schwinzer
,
Hévila
Brognaro
,
Cromarte
Rogers
,
Diogo
Melo
,
Joanna J.
Zaitseva-Doyle
,
Juraj
Knoska
,
Gisel E.
Peña-Murillo
,
Aida Rahmani
Mashhour
,
Vincent
Hennicke
,
Pontus
Fischer
,
Johanna
Hakanpää
,
Jan
Meyer
,
Philip
Gribbon
,
Bernhard
Ellinger
,
Maria
Kuzikov
,
Markus
Wolf
,
Andrea R.
Beccari
,
Gleb
Bourenkov
,
David
Von Stetten
,
Guillaume
Pompidor
,
Isabel
Bento
,
Saravanan
Panneerselvam
,
Ivars
Karpics
,
Thomas R.
Schneider
,
Maria Marta
Garcia-Alai
,
Stephan
Niebling
,
Christian
Günther
,
Christina
Schmidt
,
Robin
Schubert
,
Huijong
Han
,
Juliane
Boger
,
Diana C. F.
Monteiro
,
Linlin
Zhang
,
Xinyuanyuan
Sun
,
Jonathan
Pletzer-Zelgert
,
Jan
Wollenhaupt
,
Christian G.
Feiler
,
Manfred S.
Weiss
,
Eike-Christian
Schulz
,
Pedram
Mehrabi
,
Katarina
Karničar
,
Aleksandra
Usenik
,
Jure
Loboda
,
Henning
Tidow
,
Ashwin
Chari
,
Rolf
Hilgenfeld
,
Charlotte
Uetrecht
,
Russell
Cox
,
Andrea
Zaliani
,
Tobias
Beck
,
Matthias
Rarey
,
Stephan
Günther
,
Dusan
Turk
,
Winfried
Hinrichs
,
Henry N.
Chapman
,
Arwen R.
Pearson
,
Christian
Betzel
,
Alke
Meents
Open Access
Abstract: The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput X-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied X-ray fragment screening experiments with molecules of low complexity, our screen tested already approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six non-peptidic compounds showed antiviral activity at non-toxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.
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Apr 2021
|
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Haoyuan
Li
,
Reza
Nazari
,
Brian
Abbey
,
Roberto
Alvarez
,
Andrew
Aquila
,
Kartik
Ayyer
,
Anton
Barty
,
Peter
Berntsen
,
Johan
Bielecki
,
Alberto
Pietrini
,
Maximilian
Bucher
,
Gabriella
Carini
,
Henry N.
Chapman
,
Alice
Contreras
,
Benedikt J.
Daurer
,
Hasan
Demirci
,
Leonie
Flűckiger
,
Matthias
Frank
,
Janos
Hajdu
,
Max F.
Hantke
,
Brenda G.
Hogue
,
Ahmad
Hosseinizadeh
,
Mark S.
Hunter
,
H. Olof
Jönsson
,
Richard A.
Kirian
,
Ruslan P.
Kurta
,
Duane
Loh
,
Filipe R. N. C.
Maia
,
Adrian P.
Mancuso
,
Andrew J.
Morgan
,
Matthew
Mcfadden
,
Kerstin
Muehlig
,
Anna
Munke
,
Hemanth Kumar Narayana
Reddy
,
Carl
Nettelblad
,
Abbas
Ourmazd
,
Max
Rose
,
Peter
Schwander
,
M.
Marvin Seibert
,
Jonas A.
Sellberg
,
Raymond G.
Sierra
,
Zhibin
Sun
,
Martin
Svenda
,
Ivan A.
Vartanyants
,
Peter
Walter
,
Daniel
Westphal
,
Garth
Williams
,
P. Lourdu
Xavier
,
Chun Hong
Yoon
,
Sahba
Zaare
Open Access
Abstract: Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.
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Nov 2020
|
|
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Austin
Echelmeier
,
Jorvani
Cruz Villarreal
,
Marc
Messerschmidt
,
Daihyun
Kim
,
Jesse D.
Coe
,
Darren
Thifault
,
Sabine
Botha
,
Ana
Egatz-Gomez
,
Sahir
Gandhi
,
Gerrit
Brehm
,
Chelsie E.
Conrad
,
Debra T.
Hansen
,
Caleb
Madsen
,
Saša
Bajt
,
J. Domingo
Meza-Aguilar
,
Dominik
Oberthuer
,
Max O.
Wiedorn
,
Holger
Fleckenstein
,
Derek
Mendez
,
Juraj
Knoška
,
Jose M.
Martin-Garcia
,
Hao
Hu
,
Stella
Lisova
,
Aschkai
Allahgoli
,
Yaroslav
Gevorkov
,
Kartik
Ayyer
,
Steve
Aplin
,
Helen M.
Ginn
,
Heinz
Graafsma
,
Andrew J.
Morgan
,
Dominic
Greiffenberg
,
Alexander
Klujev
,
Torsten
Laurus
,
Jennifer
Poehlsen
,
Ulrich
Trunk
,
Davide
Mezza
,
Bernd
Schmitt
,
Manuela
Kuhn
,
Raimund
Fromme
,
Jolanta
Sztuk-Dambietz
,
Natascha
Raab
,
Steffen
Hauf
,
Alessandro
Silenzi
,
Thomas
Michelat
,
Chen
Xu
,
Cyril
Danilevski
,
Andrea
Parenti
,
Leonce
Mekinda
,
Britta
Weinhausen
,
Grant
Mills
,
Patrik
Vagovic
,
Yoonhee
Kim
,
Henry
Kirkwood
,
Richard
Bean
,
Johan
Bielecki
,
Stephan
Stern
,
Klaus
Giewekemeyer
,
Adam
Round
,
Joachim
Schulz
,
Katerina
Dörner
,
Thomas D.
Grant
,
Valerio
Mariani
,
Anton
Barty
,
Adrian P.
Mancuso
,
Uwe
Weierstall
,
John C. H.
Spence
,
Henry N.
Chapman
,
Nadia
Zatsepin
,
Petra
Fromme
,
Richard A.
Kirian
,
Alexandra
Ros
Open Access
Abstract: Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported.
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Sep 2020
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