sample-preparation-transfer-protocol-for-vacuum-long-wavelength

Sample Preparation and Transfer Protocol for In-Vacuum Long-Wavelength Crystallography on Beamline I23 at Diamond Light Source

Long-wavelength macromolecular crystallography (MX) exploits the anomalous scattering properties of elements, such as sulfur, phosphorus, potassium, ...

Diamond Light Source Ltd, Harwell Science & Innovation Campus

Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given.

Application of in situ diffraction in high-throughput structure determination platforms.

Determination of protein crystal structures requires that the phases are derived independently of the observed measurement of diffraction intensities. Many techniques have been developed to obtain phases, including heavy-atom substitution, molecular replacement and substitution during protein expression of the amino acid methionine with selenomethionine. Although the use of selenium-containing methionine has transformed the experimental determination of phases it is not always possible, either because the variant protein cannot be produced or does not crystallize. Phasing of structures by measuring the anomalous diffraction from S atoms could in theory be almost universal since almost all proteins contain methionine or cysteine. Indeed, many structures have been solved by the so-called native sulfur single-wavelength anomalous diffraction (S-SAD) phasing method. However, the anomalous effect is weak at the wavelengths where data are normally recorded (between 1 and 2 Å) and this limits the potential of this method to well diffracting crystals. Longer wavelengths increase the strength of the anomalous signal but at the cost of increasing air absorption and scatter, which degrade the precision of the anomalous measurement, consequently hindering phase determination. A new instrument, the long-wavelength beamline I23 at Diamond Light Source, was designed to work at significantly longer wavelengths compared with standard synchrotron beamlines in order to open up the native S-SAD method to projects of increasing complexity. Here, the first novel structure, that of the oxidase domain involved in the production of the natural product patellamide, solved on this beamline is reported using data collected to a resolution of 3.15 Å at a wavelength of 3.1 Å. The oxidase is an example of a protein that does not crystallize as the selenium variant and for which no suitable homology model for molecular replacement was available. Initial attempts collecting anomalous diffraction data for native sulfur phasing on a standard macromolecular crystallography beamline using a wavelength of 1.77 Å did not yield a structure. The new beamline thus has the potential to facilitate structure determination by native S-SAD phasing for what would previously have been regarded as very challenging cases with modestly diffracting crystals and low sulfur content.

Structure of the cyanobactin oxidase ThcOx from Cyanothece sp. PCC 7425, the first structure to be solved at Diamond Light Source beamline I23 by means of S-SAD.

Realtime in situ temperature monitoring in difficult experimental conditions or inaccessible environments is critical for many applications. Non-contact luminescence decay time thermometry is often the method of choice for such applications due to a favorable combination of sensitivity, accuracy and robustness. In this work, we demonstrate the feasibility of an ultrafast PbI scintillator for temperature determination, using the time structure of X-ray radiation, produced by a synchrotron. The decay kinetics of the scintillations was measured over the 8-107 K temperature range using monochromatic pulsed X-ray excitation. It is found that lead iodide exhibits a very fast and intense scintillation response due to excitons and donor-acceptor pairs, with the fast decay component varying between 0.08 and 0.5 ns - a feature that can be readily exploited for temperature monitoring. The observed temperature dependence of the decay time is discussed in terms of two possible mechanisms of thermal quenching - transition over activation barrier and phonon-assisted escape. It is concluded that the latter provides a better fit to the experimental results and is consistent with the model of luminescence processes in PbI. We evaluated the sensitivity and estimated the accuracy of the temperature determination as ca. ±6 K at 107 K, improving to ±1.4 K at 8 K. The results of this study prove the feasibility of temperature monitoring, using ultrafast scintillation of PbI excited by X-ray pulses from a synchrotron, thus enabling non-contact in-situ cryothermometry with megahertz sampling rate.

Megahertz non-contact luminescence decay time cryothermometry by means of ultrafast PbI scintillator.

The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions not only to maintain its three-dimensional fold but also to perform protein synthesis. Despite the vast biochemical data regarding the importance of metal ions for efficient protein synthesis and the increasing number of ribosome structures solved by X-ray crystallography or cryo-electron microscopy, the assignment of metal ions within the ribosome remains elusive due to methodological limitations. Here we present extensive experimental data on the potassium composition and environment in two structures of functional ribosome complexes obtained by measurement of the potassium anomalous signal at the K-edge, derived from long-wavelength X-ray diffraction data. We elucidate the role of potassium ions in protein synthesis at the three-dimensional level, most notably, in the environment of the ribosome functional decoding and peptidyl transferase centers. Our data expand the fundamental knowledge of the mechanism of ribosome function and structural integrity.

Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction.

Although often presented as taking single `snapshots' of the conformation of a protein, X-ray crystallography provides an averaged structure over time and space within the crystal. The important but difficult task of characterizing structural ensembles in crystals is typically limited to small conformational changes, such as multiple side-chain conformations. A crystallographic method was recently introduced that utilizes residual electron and anomalous density (READ) to characterize structural ensembles encompassing large-scale structural changes. Key to this method is an ability to accurately measure anomalous signals and distinguish them from noise or other anomalous scatterers. This report presents an optimized data-collection and analysis strategy for partially occupied iodine anomalous signals. Using the long-wavelength-optimized beamline I23 at Diamond Light Source, the ability to accurately distinguish the positions of anomalous scatterers with occupancies as low as ∼12% is demonstrated. The number and positions of these anomalous scatterers are consistent with previous biophysical, kinetic and structural data that suggest that the protein Im7 binds to the chaperone Spy in multiple partially occupied conformations. Finally, READ selections demonstrate that re-measured data using the new protocols are consistent with the previously characterized structural ensemble of the chaperone Spy with its client Im7. This study shows that a long-wavelength beamline results in easily validated anomalous signals that are strong enough to be used to detect and characterize highly disordered sections of crystal structures.

Identifying dynamic, partially occupied residues using anomalous scattering.

Highly efficient scintillation crystals with short decay times are indispensable for improving the performance of numerous detection and imaging instruments that use- X-rays, gamma-quanta, ionising particles or neutrons. Halide perovskites emerged recently as very promising materials for detection of ionising radiation that motivated further exploration of the materials. In this work, we report on excellent scintillation properties of CsPbBr crystals when cooled to cryogenic temperatures. The temperature dependence of luminescence spectra, decay kinetics and light yield under excitation with X-rays and α-particles was investigated. It is shown that the observed changes of spectral and kinetic characteristics of the crystal with temperature can be consistently explained by radiative decay of free excitons, bound and trapped excitons as well as electron-hole pairs originating from their disintegration. It has been found that the crystal exhibits a fast decay time constant of 1 ns at 7 K. The scintillation light yield of CsPbBr at 7 K is assessed to be 50,000 ± 10,000 ph/MeV at excitation with 12 keV X-rays and 109,000 ± 22,000 ph/MeV at excitation with α-particles of Am. This finding places CsPbBr in an excellent position for the development of a new generation of cryogenic, efficient scintillation detectors with nanosecond response time, marking a step-change in opportunities for scintillator-based applications.

Article	Year
Application of in situ diffraction in high-throughput structure determination platforms. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 25502203	2015
Structure of the cyanobactin oxidase ThcOx from Cyanothece sp. PCC 7425, the first structure to be solved at Diamond Light Source beamline I23 by means of S-SAD. Acta crystallographica. Section D, Structural biology\| PubMed ID: 27841750	2016
Megahertz non-contact luminescence decay time cryothermometry by means of ultrafast PbI scintillator. Scientific reports\| PubMed ID: 30918345	2019
Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction. Nature communications\| PubMed ID: 31175275	2019
Identifying dynamic, partially occupied residues using anomalous scattering. Acta crystallographica. Section D, Structural biology\| PubMed ID: 31793902	2019
Bright and fast scintillations of an inorganic halide perovskite CsPbBr crystal at cryogenic temperatures. Scientific reports\| PubMed ID: 32451515	2020

Vitaliy Mykhaylyk

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