I24-Microfocus Macromolecular Crystallography
Detectors
|
John
Matheson
,
Danny
Axford
,
Anna
Bergamaschi
,
Maria
Carulla
,
Nicholas
Devenish
,
Noemi
Frisina
,
Viktoria
Hinger
,
Vadym
Kedych
,
Christopher
Lane
,
Aldo
Mozzanica
,
Eva
Gimenez-Navarro
,
James
O'Hea
,
Dominic
Oram
,
Robin L.
Owen
,
David
Perl
,
Adam
Prescott
,
Bernd
Schmitt
,
Shane
Scully
,
Adam
Taylor
,
Gary
Yendell
,
Graeme
Winter
Open Access
Abstract: A Jungfrau-1M detector has undergone testing at Diamond Light Source. The Jungfrau series of detectors from PSI use integration and adaptive gain, to offer very high frame rate and dynamic range, suitable for high-flux and time-resolved measurements. They are becoming more widely used, to take advantage of increasing light source brightness. We report on our experiences in testing the performance of a Jungfrau-1M without illumination, with a laboratory X-ray tube and on a microfocus beamline. The Jungfrau-1M was found to be able to resolve single photons in the laboratory and on the beamline. It was confirmed that range switching from high to intermediate gain is associated with a discontinuity in the detector response. Two methods of dark frame subtraction were compared for their effect on minimizing this discontinuity. The Jungfrau-1M was found to be very effective for recording macromolecular crystallography diffraction patterns, with no apparent detriment from the discontinuity. The Diamond machine will be upgraded in 2028–9 and will operate at significantly higher flux than at present, necessitating increased use of integrating detectors, such as Jungfrau, in the future.
|
Mar 2026
|
|
|
|
Adam
Round
,
Pierre
Aller
,
Richard
Bean
,
Johan
Bielecki
,
Agata
Butryn
,
Nicholas E.
Devenish
,
Raphael
De Wijn
,
Thomas
Dietze
,
Katerina
Doerner
,
Fabio
Dall'Antonia
,
Gabriele
Giovanetti
,
Huijong
Han
,
Vincent
Hennicke
,
Chan
Kim
,
Yoonhee
Kim
,
Marco
Kloos
,
Jayanath C. P.
Koliyadu
,
Gabriel
Leen
,
Romain
Letrun
,
Luis
Lopez Morillo
,
Allen M.
Orville
,
Tim
Pakendorf
,
Marco
Ramilli
,
Nadja
Reimers
,
Patrick
Reinke
,
Juan
Sanchez-Weatherby
,
Tokushi
Sato
,
Robin
Schubert
,
Joachim
Schulz
,
Cedric
Signe Takem
,
Marcin
Sikorski
,
Prasad
Thute
,
Fabian
Trost
,
Oleksii
Turkot
,
Patrik
Vagovic
,
Mohammad
Vakili
,
Raul
Villanueva Guerrero
,
Henry N.
Chapman
,
Alke
Meents
,
Serguei
Molodtsov
,
Sakura
Pascarelli
,
Thomas
Tschentschera
,
Adrian
Mancuso
,
Pontus
Fischer
,
Sebastian
Guenther
Open Access
Abstract: The Single-Particle, Clusters and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) scientific instrument at the European X-Ray Free-Electron Laser (EuXFEL) became operational with user experiments in September 2017. The unique properties and capabilities of the EuXFEL, enabling megahertz data collection rates, provide more rapid data collection with improved statistics compared with other XFEL facilities. This improves the feasibility of obtaining multiple data points in time-resolved experiments and hence enables the observation of reactions in greater detail (molecular movies). In collaboration with the SFX User Consortium (SFX UC), the SPB/SFX instrument was designed to further increase user access and research outcomes. Focusing the pulses downstream of the first interaction region [described previously (Mancuso et al., 2019)], a second experiment plane is enabled, which allows for greater optimization and more efficient usage of available beam time. Additionally, the SFX UC provided further instrumentation to provide improved capabilities on SPB/SFX. The aim for additional and extended functionality for the second interaction region was to enable sample-efficient data collection at atmospheric pressure in an environment where the sample temperature and humidity can be controlled. This paper describes the extended capabilities of the downstream interaction region of the SPB/SFX instrument and its major components, in particular its X-ray focusing optics, vacuum to atmospheric pressure out-coupling, available sample delivery methods and 2D detector, and the supporting optical laser systems for pump–probe experiments.
|
Nov 2025
|
|
I24-Microfocus Macromolecular Crystallography
Detectors
|
Open Access
Abstract: The JUNGFRAU detector is a charge integrating, high-frame-rate, imaging detector developed by the PSI detector group, originally to support the SwissFEL Aramis beamline. The detector includes adaptive gain switching to give single photon sensitivity whilst also allowing sufficient analogue dynamic range to record ∼10,000 12keV photons. The use of adaptive gains requires a multi-stage data correction procedure, factoring in the pedestal and gain value for each pixel for each gain mode: at 2kHz frame rate this makes for a non-trivial undertaking.
At the SLS a data capture system for this has been developed, JUNGFRAUJOCH which uses a number of Xilinx FPGA boards to read the UDP data stream and perform the correction and the initial stage of data compression, before reading out to the CPU for compression. Whilst this is an effective solution, the technology choice of FPGA high level synthesis for programming has a very high barrier to entry. Some kind of hardware acceleration is however critical to ensure the correction and compression keep up with the data acquisition rate over the long term.
At Diamond we are also acquiring a JUNGFRAU 9M detector, to use for rotation and serial crystallography on beamline I24. This brings us to the challenge: adopt JUNGFRAUJOCH or develop an alternative system, since the wider view of high throughput computing has changed over the last few years. Here we present an alternative system build around the NVIDIA Grace Hopper Superchip (GH200) which includes a 72 ARM NEOVERSE v2 CPU cores, an NVIDIA H100 GPU and high bandwidth memory (Figure 1). The capabilities of this system allow us to consider building a data capture, correction and initial analysis system to support the JUNGFRAU 9M detector at Diamond Light Source, using far more mainstream technologies (CUDA for the accelerator programming, SLS detector for the front-end data capture) and offering the opportunity to tailor the system to fit in with the use cases being developed at Diamond Light Source beamline I24. This development also takes the opportunity to explore alternative methods for representing the data, keeping the data from modules separated allowing parallelism in data capture and analysis.
|
Oct 2025
|
|
I03-Macromolecular Crystallography
|
Open Access
Abstract: Diamond Light Source's I03 beamline now spends most of its time in "Unattended Data Collection" mode. To maximise throughput, it is critical that as little time is spent waiting for x-ray centering as possible. In this talk, I will describe the GPU-based fast-feedback service that we have built, how we integrated it into our wider acquisition and analysis systems, and how we plan to evolve it for future needs.
|
Oct 2025
|
|
|
|
Jon
Agirre
,
Mihaela
Atanasova
,
Haroldas
Bagdonas
,
Charles B.
Ballard
,
Arnaud
Basle
,
James
Beilsten-Edmands
,
Rafael J.
Borges
,
David G.
Brown
,
J. Javier
Burgos-Marmol
,
John M.
Berrisford
,
Paul S.
Bond
,
Iracema
Caballero
,
Lucrezia
Catapano
,
Grzegorz
Chojnowski
,
Atlanta G.
Cook
,
Kevin D.
Cowtan
,
Tristan I.
Croll
,
Judit É.
Debreczeni
,
Nicholas E.
Devenish
,
Eleanor J.
Dodson
,
Tarik R.
Drevon
,
Paul
Emsley
,
Gwyndaf
Evans
,
Phil R.
Evans
,
Maria
Fando
,
James
Foadi
,
Luis
Fuentes-Montero
,
Elspeth F.
Garman
,
Markus
Gerstel
,
Richard J.
Gildea
,
Kaushik
Hatti
,
Maarten L.
Hekkelman
,
Philipp
Heuser
,
Soon Wen
Hoh
,
Michael A.
Hough
,
Huw T.
Jenkins
,
Elisabet
Jiménez
,
Robbie P.
Joosten
,
Ronan M.
Keegan
,
Nicholas
Keep
,
Eugene B.
Krissinel
,
Petr
Kolenko
,
Oleg
Kovalevskiy
,
Victor S.
Lamzin
,
David M.
Lawson
,
Andrey
Lebedev
,
Andrew G. W.
Leslie
,
Bernhard
Lohkamp
,
Fei
Long
,
Martin
Maly
,
Airlie
Mccoy
,
Stuart J.
Mcnicholas
,
Ana
Medina
,
Claudia
Millán
,
James W.
Murray
,
Garib N.
Murshudov
,
Robert A.
Nicholls
,
Martin E. M.
Noble
,
Robert
Oeffner
,
Navraj S.
Pannu
,
James M.
Parkhurst
,
Nicholas
Pearce
,
Joana
Pereira
,
Anastassis
Perrakis
,
Harold R.
Powell
,
Randy J.
Read
,
Daniel J.
Rigden
,
William
Rochira
,
Massimo
Sammito
,
Filomeno
Sanchez Rodriguez
,
George M.
Sheldrick
,
Kathryn L.
Shelley
,
Felix
Simkovic
,
Adam J.
Simpkin
,
Pavol
Skubak
,
Egor
Sobolev
,
Roberto A.
Steiner
,
Kyle
Stevenson
,
Ivo
Tews
,
Jens M. H.
Thomas
,
Andrea
Thorn
,
Josep Triviño
Valls
,
Ville
Uski
,
Isabel
Uson
,
Alexei
Vagin
,
Sameer
Velankar
,
Melanie
Vollmar
,
Helen
Walden
,
David
Waterman
,
Keith S.
Wilson
,
Martyn
Winn
,
Graeme
Winter
,
Marcin
Wojdyr
,
Keitaro
Yamashita
Open Access
Abstract: The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
|
Jun 2023
|
|
I24-Microfocus Macromolecular Crystallography
|
James
Baxter
,
Christopher D. M.
Hutchison
,
Karim
Maghlaoui
,
Violeta
Cordon-Preciado
,
R. Marc L.
Morgan
,
Pierre
Aller
,
Agata
Butryn
,
Danny
Axford
,
Sam
Horrell
,
Robin L.
Owen
,
Selina L. S.
Storm
,
Nicholas E.
Devenish
,
Jasper J.
Van Thor
Diamond Proposal Number(s):
[17221]
Open Access
Abstract: The chromophores of reversibly switchable fluorescent proteins (rsFPs) undergo photoisomerization of both the trans and cis forms. Concurrent with cis/trans photoisomerisation, rsFPs typically become protonated on the phenolic oxygen resulting in a blue shift of the absorption. A synthetic rsFP referred to as rsEospa, derived from EosFP family, displays the same spectroscopic behavior as the GFP-like rsFP Dronpa at pH 8.4 and involves the photoconversion between nonfluorescent neutral and fluorescent anionic chromophore states. Millisecond time-resolved synchrotron serial crystallography of rsEospa at pH 8.4 shows that photoisomerization is accompanied by rearrangements of the same three residues as seen in Dronpa. However, at pH 5.5 we observe that the OFF state is identified as the cationic chromophore with additional protonation of the imidazolinone nitrogen which is concurrent with a newly formed hydrogen bond with the Glu212 carboxylate side chain. FTIR spectroscopy resolves the characteristic up-shifted carbonyl stretching frequency at 1713 cm–1 for the cationic species. Electronic spectroscopy furthermore distinguishes the cationic absorption band at 397 nm from the neutral species at pH 8.4 seen at 387 nm. The observation of photoisomerization of the cationic chromophore state demonstrates the conical intersection for the electronic configuration, where previously fluorescence was proposed to be the main decay route for states containing imidazolinone nitrogen protonation. We present the full time-resolved room-temperature X-ray crystallographic, FTIR, and UV/vis assignment and photoconversion modeling of rsEospa.
|
Nov 2022
|
|
|
|
Open Access
Abstract: The DIALS software for the processing of X-ray diffraction data is presented, with an emphasis on how the suite may be used as a toolkit for data processing. The description starts with an overview of the history and intent of the toolkit, usage as an automated system, command-line use, and ultimately how new tools can be written using the API to perform bespoke analysis. Consideration is also made to the application of DIALS to techniques outside of macromolecular X-ray crystallography.
|
Nov 2021
|
|
I24-Microfocus Macromolecular Crystallography
|
Agata
Butryn
,
Philipp S.
Simon
,
Pierre
Aller
,
Philip
Hinchliffe
,
Ramzi N.
Massad
,
Gabriel
Leen
,
Catherine L.
Tooke
,
Isabel
Bogacz
,
In-Sik
Kim
,
Asmit
Bhowmick
,
Aaron S.
Brewster
,
Nicholas E.
Devenish
,
Jurgen
Brem
,
Jos J. A. G.
Kamps
,
Pauline A.
Lang
,
Patrick
Rabe
,
Danny
Axford
,
John H.
Beale
,
Bradley
Davy
,
Ali
Ebrahim
,
Julien
Orlans
,
Selina L. S.
Storm
,
Tiankun
Zhou
,
Shigeki
Owada
,
Rie
Tanaka
,
Kensuke
Tono
,
Gwyndaf
Evans
,
Robin L.
Owen
,
Frances A.
Houle
,
Nicholas K.
Sauter
,
Christopher J.
Schofield
,
James
Spencer
,
Vittal K.
Yachandra
,
Junko
Yano
,
Jan F.
Kern
,
Allen M.
Orville
Diamond Proposal Number(s):
[19458, 25260]
Open Access
Abstract: Serial femtosecond crystallography has opened up many new opportunities in structural biology. In recent years, several approaches employing light-inducible systems have emerged to enable time-resolved experiments that reveal protein dynamics at high atomic and temporal resolutions. However, very few enzymes are light-dependent, whereas macromolecules requiring ligand diffusion into an active site are ubiquitous. In this work we present a drop-on-drop sample delivery system that enables the study of enzyme-catalyzed reactions in microcrystal slurries. The system delivers ligand solutions in bursts of multiple picoliter-sized drops on top of a larger crystal-containing drop inducing turbulent mixing and transports the mixture to the X-ray interaction region with temporal resolution. We demonstrate mixing using fluorescent dyes, numerical simulations and time-resolved serial femtosecond crystallography, which show rapid ligand diffusion through microdroplets. The drop-on-drop method has the potential to be widely applicable to serial crystallography studies, particularly of enzyme reactions with small molecule substrates.
|
Jul 2021
|
|
I24-Microfocus Macromolecular Crystallography
Data acquisition
|
Open Access
Abstract: Serial data collection is a relatively new technique for synchrotron users. A user manual for fixed target data collection at I24, Diamond Light Source is presented with detailed step-by-step instructions, figures, and videos for smooth data collection.
|
Feb 2021
|
|
I24-Microfocus Macromolecular Crystallography
|
Open Access
Abstract: With the increasing trend of using microcrystals and intense microbeams at synchrotron X-ray beamlines, radiation damage becomes a more pressing problem. Theoretical calculations show that the photoelectrons that primarily cause damage can escape microcrystals. This effect would become more pronounced with decreasing crystal size as well as at higher energies. To prove this effect, data from cryocooled lysozyme crystals of dimensions 5 × 3 × 3 and 20 × 8 × 8 µm mounted on cryo-transmission electron microscopy (cryo-TEM) grids were collected at 13.5 and 20.1 keV using a PILATUS CdTe 2M detector, which has a similar quantum efficiency at both energies. Accurate absorbed doses were calculated through the direct measurement of individual crystal sizes using scanning electron microscopy after the experiment and characterization of the X-ray microbeam. The crystal lifetime was then quantified based on the D1/2 metric. In this first systematic study, a longer crystal lifetime for smaller crystals was observed and crystal lifetime increased at higher X-ray energies, supporting the theoretical predictions of photoelectron escape. The use of detector technologies specifically optimized for data collection at energies above 20 keV allows the theoretically predicted photoelectron escape to be quantified and exploited, guiding future beamline-design choices.
|
Jan 2020
|
|
