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Arnal RD, Millane RP. Ab initio reconstruction from one-dimensional crystal diffraction data. Acta Crystallogr A Found Adv 2022; 78:249-261. [PMID: 35502716 PMCID: PMC9062830 DOI: 10.1107/s2053273322001942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/18/2022] [Indexed: 11/11/2022] Open
Abstract
Filamentary and rod-like assemblies are ubiquitous in biological systems, and single such assemblies can form one-dimensional (1D) crystals. New, intense X-ray sources, such as X-ray free-electron lasers, make it feasible to measure diffraction data from single 1D crystals. Such experiments would present some advantages, since cylindrical averaging of the diffraction data in conventional fiber diffraction analysis is avoided, there is coherent signal amplification relative to single-particle imaging, and the diffraction data are oversampled compared with those from a 3D crystal so that the phase problem is better determined than for a 3D crystal [Millane (2017). Acta Cryst. A73, 140-150]. Phasing of 1D crystal diffraction data is examined, by simulation, using an iterative projection algorithm. Ab initio phasing is feasible with realistic noise levels and little envelope information is required if a shrink-wrap algorithm is also incorporated. Some practical aspects of the proposed experiments are explored.
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Affiliation(s)
- Romain D. Arnal
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
| | - Rick P. Millane
- Computational Imaging Group, Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
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2
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Knoška J, Adriano L, Awel S, Beyerlein KR, Yefanov O, Oberthuer D, Peña Murillo GE, Roth N, Sarrou I, Villanueva-Perez P, Wiedorn MO, Wilde F, Bajt S, Chapman HN, Heymann M. Ultracompact 3D microfluidics for time-resolved structural biology. Nat Commun 2020; 11:657. [PMID: 32005876 PMCID: PMC6994545 DOI: 10.1038/s41467-020-14434-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/10/2019] [Indexed: 11/23/2022] Open
Abstract
To advance microfluidic integration, we present the use of two-photon additive manufacturing to fold 2D channel layouts into compact free-form 3D fluidic circuits with nanometer precision. We demonstrate this technique by tailoring microfluidic nozzles and mixers for time-resolved structural biology at X-ray free-electron lasers (XFELs). We achieve submicron jets with speeds exceeding 160 m s-1, which allows for the use of megahertz XFEL repetition rates. By integrating an additional orifice, we implement a low consumption flow-focusing nozzle, which is validated by solving a hemoglobin structure. Also, aberration-free in operando X-ray microtomography is introduced to study efficient equivolumetric millisecond mixing in channels with 3D features integrated into the nozzle. Such devices can be printed in minutes by locally adjusting print resolution during fabrication. This technology has the potential to permit ultracompact devices and performance improvements through 3D flow optimization in all fields of microfluidic engineering.
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Affiliation(s)
- Juraj Knoška
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Luigi Adriano
- DESY, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
- EuXFEL, Sample Environment & Characterization Group, European XFEL Holzkoppel 4, 22869, Schenefeld, Germany
| | - Salah Awel
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- CUI, Center for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany
| | - Kenneth R Beyerlein
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, 22761, Germany
| | - Oleksandr Yefanov
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dominik Oberthuer
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Gisel E Peña Murillo
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Nils Roth
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Iosifina Sarrou
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Pablo Villanueva-Perez
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Synchrotron Radiation Research, Lund University, Box 118, SE-221 00, Lund, Sweden
| | - Max O Wiedorn
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Fabian Wilde
- Helmholtz-Zentrum Geesthacht, Institut für Werkstoffforschung, Max-Planck-Straße. 1, 21502, Geesthacht, Germany
| | - Saša Bajt
- DESY, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607, Hamburg, Germany
| | - Henry N Chapman
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
- CUI, Center for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany.
| | - Michael Heymann
- CFEL, Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.
- IBBS, Institut für Biomaterialien und Biomolekulare Systeme, Universität Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany.
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3
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Hu J, Sun H, Hao H, Zheng Q. Prediction of fibril formation by early-stage amyloid peptide aggregation. J Pharm Anal 2019; 10:194-199. [PMID: 32373391 PMCID: PMC7193079 DOI: 10.1016/j.jpha.2019.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 11/19/2019] [Accepted: 12/11/2019] [Indexed: 11/04/2022] Open
Abstract
Amyloid fibrils are found in systemic amyloidosis diseases such as Alzheimer’s disease, Parkinson’s disease, and type II diabetes. Currently, these diseases are diagnosed by observation of fibrils or plaques, which is an ineffective method for early diagnosis and treatment of disease. The goal of this study was to develop a simple and quick method to predict the possibility and speed of fibril formation before its occurrence. Oligomers generated from seven representative peptide segments were first isolated and detected by ion-mobility mass spectrometry (IM-MS). Then, their assemblies were disrupted using formic acid (FA). Interestingly, oligomers that showed small ion intensity changes upon FA addition had rapid fibril formation. By contrast, oligomers that had large ion intensity changes generated fibrils slowly. Two control peptides (aggregation/no fibrils and no aggregation/no fibrils) did not show changes in their ion intensities, which confirmed the ability of this method to predict amyloid formation. In summary, the developed method correlated MS intensity ratio changes of peptide oligomers on FA addition with their amyloid propensities. This method will be useful for monitoring peptide/protein aggregation behavior and essential for their mechanism studies. Co-populated oligomers are differentiated by IM-MS. Oligomers that showed small ranges of fold change had rapid fibril formation. Oligomers that had large ranges of fold change generated fibrils slowly. Fold changes of oligomers are representative to their aggregation propensities.
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Affiliation(s)
- Jiaojiao Hu
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu, 210009, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu, 210009, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu, 210009, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu, 210009, China
| | - Haiping Hao
- Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu, 210009, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu, 210009, China
| | - Qiuling Zheng
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu, 210009, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu, 210009, China
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4
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Echelmeier A, Sonker M, Ros A. Microfluidic sample delivery for serial crystallography using XFELs. Anal Bioanal Chem 2019; 411:6535-6547. [PMID: 31250066 DOI: 10.1007/s00216-019-01977-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/23/2019] [Accepted: 06/12/2019] [Indexed: 12/18/2022]
Abstract
Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) is an emerging field for structural biology. One of its major impacts lies in the ability to reveal the structure of complex proteins previously inaccessible with synchrotron-based crystallography techniques and allowing time-resolved studies from femtoseconds to seconds. The nature of this serial technique requires new approaches for crystallization, data analysis, and sample delivery. With continued advancements in microfabrication techniques, various developments have been reported in the past decade for innovative and efficient microfluidic sample delivery for crystallography experiments using XFELs. This article summarizes the recent developments in microfluidic sample delivery with liquid injection and fixed-target approaches, which allow exciting new research with XFELs. Graphical abstract.
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Affiliation(s)
- Austin Echelmeier
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Box 871604, Tempe, AZ, 85287-1604, USA. .,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Box 875001, Tempe, AZ, 85287-7401, USA.
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5
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Abstract
X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.
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Affiliation(s)
- Henry N. Chapman
- Center for Free-Electron Laser Science, DESY, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, 22761 Hamburg, Germany
- Centre for Ultrafast Imaging, University of Hamburg, 22761 Hamburg, Germany
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6
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Brändén G, Hammarin G, Harimoorthy R, Johansson A, Arnlund D, Malmerberg E, Barty A, Tångefjord S, Berntsen P, DePonte DP, Seuring C, White TA, Stellato F, Bean R, Beyerlein KR, Chavas LMG, Fleckenstein H, Gati C, Ghoshdastider U, Gumprecht L, Oberthür D, Popp D, Seibert M, Tilp T, Messerschmidt M, Williams GJ, Loh ND, Chapman HN, Zwart P, Liang M, Boutet S, Robinson RC, Neutze R. Coherent diffractive imaging of microtubules using an X-ray laser. Nat Commun 2019; 10:2589. [PMID: 31197138 PMCID: PMC6565740 DOI: 10.1038/s41467-019-10448-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 05/02/2019] [Indexed: 01/09/2023] Open
Abstract
X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2 nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4 nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.
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Affiliation(s)
- Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden.
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Alexander Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Erik Malmerberg
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, 94720, Berkeley, CA, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Stefan Tångefjord
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, 22761, Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Francesco Stellato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Kenneth R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Leonard M G Chavas
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore, Singapore
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - David Popp
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore, Singapore
| | - Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Thomas Tilp
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - N Duane Loh
- Department of Physics, National University of Singapore, 117551, Singapore, Singapore
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, 22761, Hamburg, Germany.,Department of Physics, University of Hamburg, 22761, Hamburg, Germany
| | - Peter Zwart
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, 94720, Berkeley, CA, USA
| | - Mengning Liang
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore, Singapore.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden.
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Martiel I, Müller-Werkmeister HM, Cohen AE. Strategies for sample delivery for femtosecond crystallography. Acta Crystallogr D Struct Biol 2019; 75:160-177. [PMID: 30821705 PMCID: PMC6400256 DOI: 10.1107/s2059798318017953] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/19/2018] [Indexed: 11/11/2022] Open
Abstract
Highly efficient data-collection methods are required for successful macromolecular crystallography (MX) experiments at X-ray free-electron lasers (XFELs). XFEL beamtime is scarce, and the high peak brightness of each XFEL pulse destroys the exposed crystal volume. It is therefore necessary to combine diffraction images from a large number of crystals (hundreds to hundreds of thousands) to obtain a final data set, bringing about sample-refreshment challenges that have previously been unknown to the MX synchrotron community. In view of this experimental complexity, a number of sample delivery methods have emerged, each with specific requirements, drawbacks and advantages. To provide useful selection criteria for future experiments, this review summarizes the currently available sample delivery methods, emphasising the basic principles and the specific sample requirements. Two main approaches to sample delivery are first covered: (i) injector methods with liquid or viscous media and (ii) fixed-target methods using large crystals or using microcrystals inside multi-crystal holders or chips. Additionally, hybrid methods such as acoustic droplet ejection and crystal extraction are covered, which combine the advantages of both fixed-target and injector approaches.
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Affiliation(s)
- Isabelle Martiel
- Swiss Light Source, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Henrike M. Müller-Werkmeister
- Institute of Chemistry – Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam-Golm, Germany
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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8
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Fewster PF. Response to Fraser & Wark's comments on A new theory for X-ray diffraction. Acta Crystallogr A Found Adv 2018; 74:457-465. [PMID: 30182933 PMCID: PMC6123939 DOI: 10.1107/s2053273318007489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/17/2018] [Indexed: 11/10/2022] Open
Abstract
The criticisms of my theory, as given by Fraser & Wark [(2018), Acta Cryst. A74, 447-456], are built on a misunderstanding of the concept and the methodology I have used. The assumption they have made rules out my description from which they conclude that my theory is proved to be wrong. They assume that I have misunderstood the diffraction associated with the shape of a crystal and my calculation is only relevant to a parallelepiped and even that I have got wrong. It only appears wrong to Fraser & Wark because the effect I predict has nothing to do with the crystal shape. The effect though can be measured as well as the crystal shape effects. This response describes my reasoning behind the theory, how it can be related to the Ewald sphere construction, and the build-up of the full diffraction pattern from all the scatterers in a stack of planes. It is the latter point that makes the Fraser & Wark analysis incomplete. The description given in this article describes my approach much more precisely with reference to the Ewald sphere construction. Several experiments are described that directly measure the predictions of the new theory, which are explained with reference to the Ewald sphere description. In its simplest terms the new theory can be considered as giving a thickness to the Ewald sphere surface, whereas in the conventional theory it has no thickness. Any thickness immediately informs us that the scattering from a peak at the Bragg angle does not have to be in the Bragg condition to be observed. I believe the conventional theory is a very good approximation, but as soon as it is tested with careful experiments it is shown to be incomplete. The new theory puts forward the idea that there is persistent intensity at the Bragg scattering angle outside the Bragg condition. This intensity is weak (∼10-5) but can be observed in careful laboratory experiments, despite being on the limit of observation, yet it has a profound impact on how we should interpret diffraction patterns.
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9
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Fewster PF. Estimating the structure factors in X-ray diffraction. Acta Crystallogr A Found Adv 2018; 74:481-498. [PMID: 30182935 PMCID: PMC6123942 DOI: 10.1107/s2053273318007593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 05/21/2018] [Indexed: 11/10/2022] Open
Abstract
This article takes the concepts of the `new diffraction theory' [Fewster (2014). Acta Cryst. A70, 257-282] and examines the implications for the interpretation of experimental results and the estimation of structure factors. Further experimental evidence is included to justify the conclusions in the theory, showing that the residual intensity at twice the Bragg angle is a diffraction effect and not associated with the crystal shape. This `enhancement' effect is independent of whether kinematical or dynamical theories are applied and can lead to a clearer understanding of how the dynamical effects are suppressed in imperfect crystals. By applying the idea that the higher-order peaks are due to path lengths of nλ, it is shown that `systematically absent' reflections in the conventional theory may not be absent. Because this new theory considers the intensity to be more distributed, it suggests that the entire structure factor can be difficult to capture by experiment. This article suggests some routes to achieve a good approximation of the structure factors for typical methods of data collection. Any measurement of intensity with background removal will exclude some of the distributed intensity, again leading to an underestimate of the structure factors, and therefore the missing intensity needs to be estimated.
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10
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Femtosecond X-ray coherent diffraction of aligned amyloid fibrils on low background graphene. Nat Commun 2018; 9:1836. [PMID: 29743480 PMCID: PMC5943278 DOI: 10.1038/s41467-018-04116-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/03/2018] [Indexed: 11/09/2022] Open
Abstract
Here we present a new approach to diffraction imaging of amyloid fibrils, combining a free-standing graphene support and single nanofocused X-ray pulses of femtosecond duration from an X-ray free-electron laser. Due to the very low background scattering from the graphene support and mutual alignment of filaments, diffraction from tobacco mosaic virus (TMV) filaments and amyloid protofibrils is obtained to 2.7 Å and 2.4 Å resolution in single diffraction patterns, respectively. Some TMV diffraction patterns exhibit asymmetry that indicates the presence of a limited number of axial rotations in the XFEL focus. Signal-to-noise levels from individual diffraction patterns are enhanced using computational alignment and merging, giving patterns that are superior to those obtainable from synchrotron radiation sources. We anticipate that our approach will be a starting point for further investigations into unsolved structures of filaments and other weakly scattering objects.
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