Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2Aadenosine receptor (A2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suitesCheetahandCrystFELenabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.

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De novo protein structure determination by heavy-atom soaking in lipidic cubic phase and SIRAS phasing using serial synchrotron crystallography

IUCrJ ◽

10.1107/s2052252518009223 ◽

2018 ◽

Vol 5 (5) ◽

pp. 524-530 ◽

Cited By ~ 4

Author(s):

S. Botha ◽

D. Baitan ◽

K. E. J. Jungnickel ◽

D. Oberthür ◽

C. Schmidt ◽

...

Keyword(s):

Synchrotron Radiation ◽

Data Collection ◽

Diffraction Data ◽

Heavy Atom ◽

Proteinase K ◽

Cubic Phase ◽

Anomalous Scattering ◽

Experimental Phasing ◽

Lipidic Cubic Phase ◽

Serial Crystallography

During the past few years, serial crystallography methods have undergone continuous development and serial data collection has become well established at high-intensity synchrotron-radiation beamlines and XFEL radiation sources. However, the application of experimental phasing to serial crystallography data has remained a challenging task owing to the inherent inaccuracy of the diffraction data. Here, a particularly gentle method for incorporating heavy atoms into micrometre-sized crystals utilizing lipidic cubic phase (LCP) as a carrier medium is reported. Soaking in LCP prior to data collection offers a new, efficient and gentle approach for preparing heavy-atom-derivative crystals directly before diffraction data collection using serial crystallography methods. This approach supports effective phasing by utilizing a reasonably low number of diffraction patterns. Using synchrotron radiation and exploiting the anomalous scattering signal of mercury for single isomorphous replacement with anomalous scattering (SIRAS) phasing resulted in high-quality electron-density maps that were sufficient for building a complete structural model of proteinase K at 1.9 Å resolution using automatic model-building tools.

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Hydrated metal(II) complexes of N-(6-amino-3,4-dihydro-3-methyl-5-nitroso-4-oxopyrimidin-2-yl) derivatives of glycine, glycylglycine, threonine, serine, valine and methionine: a monomeric complex and coordination polymers in one, two and three dimensions linked by hydrogen bonding. Corrigendum

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768105042059 ◽

2006 ◽

Vol 62 (1) ◽

pp. 165-165

Author(s):

M. Luz Godino Salido ◽

Paloma Arranz Mascarós ◽

Rafaél López Garzón ◽

M. Dolores Gutiérrez Valero ◽

John N. Low ◽

...

Keyword(s):

Hydrogen Bonding ◽

Synchrotron Radiation ◽

Data Collection ◽

Coordination Polymers ◽

Data Reduction ◽

Three Dimensions ◽

Compound Viii ◽

Monomeric Complex ◽

Cell Refinement ◽

Derivatives Of

Some of the data collection details for compound (VIII) were incorrectly given in Table 1 of Godino Salido et al. (2004). The data for compound VIII in this paper were collected using synchrotron radiation at the Daresbury SRS station 9.8, λ = 0.6935 Å (Cernik et al., 1997; Clegg, 2000). The data were collected using a Bruker SMART 1K CCD diffractometer using ω rotation with narrow frames. The computer program used in the data collection was SMART (Bruker, 2001) and for cell refinement and data reduction SAINT (Bruker, 2001).

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Protein microcrystallography using synchrotron radiation

IUCrJ ◽

10.1107/s2052252517008193 ◽

2017 ◽

Vol 4 (5) ◽

pp. 529-539 ◽

Cited By ~ 30

Author(s):

Masaki Yamamoto ◽

Kunio Hirata ◽

Keitaro Yamashita ◽

Kazuya Hasegawa ◽

Go Ueno ◽

...

Keyword(s):

Synchrotron Radiation ◽

Data Collection ◽

Diffraction Data ◽

Structure Determination ◽

Structural Features ◽

X Ray ◽

Data Collection Strategy ◽

Technological Developments ◽

Novel Method

The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as smallin mesocrystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.

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High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source

IUCrJ ◽

10.1107/s205225251900263x ◽

2019 ◽

Vol 6 (3) ◽

pp. 412-425 ◽

Cited By ~ 17

Author(s):

Jose M. Martin-Garcia ◽

Lan Zhu ◽

Derek Mendez ◽

Ming-Yue Lee ◽

Eugene Chun ◽

...

Keyword(s):

Synchrotron Radiation ◽

Radiation Source ◽

Structural Changes ◽

High Viscosity ◽

Synchrotron Radiation Source ◽

Proteinase K ◽

Moderate Increase ◽

Time Resolved ◽

X Ray ◽

Serial Crystallography

Since the first successful serial crystallography (SX) experiment at a synchrotron radiation source, the popularity of this approach has continued to grow showing that third-generation synchrotrons can be viable alternatives to scarce X-ray free-electron laser sources. Synchrotron radiation flux may be increased ∼100 times by a moderate increase in the bandwidth (`pink beam' conditions) at some cost to data analysis complexity. Here, we report the first high-viscosity injector-based pink-beam SX experiments. The structures of proteinase K (PK) and A2A adenosine receptor (A2AAR) were determined to resolutions of 1.8 and 4.2 Å using 4 and 24 consecutive 100 ps X-ray pulse exposures, respectively. Strong PK data were processed using existing Laue approaches, while weaker A2AAR data required an alternative data-processing strategy. This demonstration of the feasibility presents new opportunities for time-resolved experiments with microcrystals to study structural changes in real time at pink-beam synchrotron beamlines worldwide.

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Visualization of protein crystals by high-energy phase-contrast X-ray imaging

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798319011379 ◽

2019 ◽

Vol 75 (11) ◽

pp. 947-958 ◽

Cited By ~ 4

Author(s):

Maxim Polikarpov ◽

Gleb Bourenkov ◽

Irina Snigireva ◽

Anatoly Snigirev ◽

Sophie Zimmermann ◽

...

Keyword(s):

Synchrotron Radiation ◽

Data Collection ◽

Diffraction Data ◽

Phase Contrast ◽

High Energy ◽

Protein Crystals ◽

Cubic Phase ◽

Macromolecular Crystallography ◽

X Ray ◽

X Ray Imaging

For the extraction of the best possible X-ray diffraction data from macromolecular crystals, accurate positioning of the crystals with respect to the X-ray beam is crucial. In addition, information about the shape and internal defects of crystals allows the optimization of data-collection strategies. Here, it is demonstrated that the X-ray beam available on the macromolecular crystallography beamline P14 at the high-brilliance synchrotron-radiation source PETRA III at DESY, Hamburg, Germany can be used for high-energy phase-contrast microtomography of protein crystals mounted in an optically opaque lipidic cubic phase matrix. Three-dimensional tomograms have been obtained at X-ray doses that are substantially smaller and on time scales that are substantially shorter than those used for diffraction-scanning approaches that display protein crystals at micrometre resolution. Adding a compound refractive lens as an objective to the imaging setup, two-dimensional imaging at sub-micrometre resolution has been achieved. All experiments were performed on a standard macromolecular crystallography beamline and are compatible with standard diffraction data-collection workflows and apparatus. Phase-contrast X-ray imaging of macromolecular crystals could find wide application at existing and upcoming low-emittance synchrotron-radiation sources.

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Data-collection facility for study of biological macromolecules using synchrotron radiation

Acta Crystallographica Section A Foundations of Crystallography ◽

10.1107/s0108767384099530 ◽

1984 ◽

Vol 40 (a1) ◽

pp. C10-C10

Author(s):

R. M. Sweet ◽

J. B. Hastings ◽

W. C. Thomlinson ◽

D. S. Wise ◽

B. P. Schoenborn

Keyword(s):

Synchrotron Radiation ◽

Data Collection ◽

Biological Macromolecules

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A measuring procedure for single-crystal diffraction using synchrotron radiation

Journal of Applied Crystallography ◽

10.1107/s0021889889000610 ◽

1989 ◽

Vol 22 (4) ◽

pp. 382-383 ◽

Cited By ~ 1

Author(s):

M. Wendschuh-Josties ◽

R. Wulf

Keyword(s):

Synchrotron Radiation ◽

Data Collection ◽

Single Crystal ◽

Real Time ◽

Data Reduction ◽

Single Crystal Diffraction ◽

Precise Location ◽

Precise Data ◽

Measuring Procedure

The use of synchrotron radiation (SR) for single-crystal diffraction measurements requires special features of both the instrumentation and the measuring procedure. This paper describes a new algorithm for data collection developed for synchrotron radiation. It has been used successfully at the five-circle diffractometer at HASYLAB (DESY, Hamburg). The main features are: precise location of the reflection position, determination of the measuring parameters by pre-scanning, subsequent fine scanning, and real-time monitoring of several parameters of the beam conditions for data reduction. This allows fast and precise data collection.

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Structure determination from lipidic cubic phase embedded microcrystals by MicroED

10.1101/724575 ◽

2019 ◽

Cited By ~ 1

Author(s):

Lan Zhu ◽

Guanhong Bu ◽

Liang Jing ◽

Dan Shi ◽

Tamir Gonen ◽

...

Keyword(s):

High Resolution ◽

Electron Diffraction ◽

Structure Determination ◽

Model System ◽

Proteinase K ◽

Electron Diffraction Data ◽

Cubic Phase ◽

High Quality ◽

Small Crystals ◽

Lipidic Cubic Phase

AbstractThe lipidic cubic phase (LCP) technique has proved to facilitate the growth of high-quality crystals that are otherwise difficult to grow by other methods. Because crystals grown in LCP can be limited in size, improved techniques for structure determination from these small crystals are important. Microcrystal electron diffraction (MicroED) is a technique that uses a cryo-TEM to collect electron diffraction data and determine high-resolution structures from very thin micro and nanocrystals. In this work, we have used modified LCP and MicroED protocols to analyze crystals embedded in LCP. Proteinase K in LCP was used as a model system, and several LCP sample preparation strategies were tested. Among these, treatment with 2-Methyl-2,4-pentanediol (MPD) and lipase were both able to reduce the viscosity of the LCP and produce quality cryo-EM grids with well-diffracting crystals. These results set the stage for the use of MicroED to analyze other microcrystalline samples grown in LCP.

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Probing structural chirality with high-energy synchrotron radiation

Journal of Applied Crystallography ◽

10.1107/s1600576716006282 ◽

2016 ◽

Vol 49 (3) ◽

pp. 918-922 ◽

Cited By ~ 3

Author(s):

Vadim Dyadkin ◽

Jon Wright ◽

Philip Pattison ◽

Dmitry Chernyshov

Keyword(s):

Synchrotron Radiation ◽

Data Collection ◽

Single Crystal ◽

Structure Determination ◽

Resonant Scattering ◽

High Energy ◽

Similar Data ◽

The Absolute ◽

Scattering Contribution ◽

Absolute Structure

The absolute structure has been determined for MnSi with data collected using synchrotron radiation withE= 78.3 keV (0.158 Å). At this energy, the resonant scattering contribution from MnSi is very small (f′Mn= −0.0397,f′′Mn= 0.0385,f′Si = −0.0197,f′′Si= 0.0027), but the large number of observed Bijvoet differences together with a wideQrange make absolute structure determination possible. A comparison with the data collected atE= 18 keV (0.68 Å) (f′Mn= 0.2858,f′′Mn= 0.6739,f′Si= 0.0653,f′′Si= 0.0646) for the same crystal shows the correctness of the absolute structure measured at the higher energy. A similar data collection has also been done atE= 65.3 keV (0.19 Å) for a single crystal of Fe0.7Co0.3Si with known absolute structure. In all cases, the absolute structure was correctly determined by analysing the statistical distribution of the chirality measure. Statistical descriptors of the refinements, the Flack parameter and the distribution of Parsons quotients are discussed for all presented experiments.

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ANALISIS PERANGKAT PEMBELAJARAN GURU PENDIDIKAN AGAMA ISLAM BERDASARKAN KURIKULUM 2013 DI SMP NEGERI 1 PERCUT SEI TUAN DELI SERDANG

ANSIRU PAI : Pengembangan Profesi Guru Pendidikan Agama Islam ◽

10.30821/ansiru.v3i2.5850 ◽

2019 ◽

Vol 3 (2) ◽

pp. 62

Author(s):

Nur Aini

Keyword(s):

Data Collection ◽

Religious Education ◽

Data Reduction ◽

Qualitative Approach ◽

Implementation Plan ◽

Analysis Technique ◽

Collection Data

The purpose of this study was to determine: (1) Suitability of 2013 Curriculum Annual Program Preparation, (2) Suitability of Compilation of the 2013 Curriculum Semester Program. (3) Appropriate components of the Learning Implementation Plan (RPP) based on Permendikbud No.22 2016. The approach used in this study is a qualitative approach The data analysis technique used is data collection, data reduction and data presentation conclusions. The technique of guaranteeing the validity of the data is done by checking trust, checking examination and checking dependency. The results of the study can be concluded that the results of the Analysis of Suitability of Annual Programming, Semester Program, and Learning Implementation Plan can be categorized as "In Accordance" because the results are obtained based on the scores of the Annual Program, Semester Program and Learning Implementation Plan (RPP) compiled by the teacher Islamic religious education in SMP Negeri 1 Percut Sei Tuan Deli Serdang.

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