Crystallization of ApoA1 and ApoE4 nanolipoprotein particles and initial XFEL-based structural studies

Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via HDL and LDL maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics and develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar in characteristics to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.

A fixed-target platform for serial femtosecond crystallography in a hydrated environment

For serial femtosecond crystallography at X-ray free-electron lasers, which entails collection of single-pulse diffraction patterns from a constantly refreshed supply of microcrystalline sample, delivery of the sample into the X-ray beam path while maintaining low background remains a technical challenge for some experiments, especially where this methodology is applied to relatively low-ordered samples or those difficult to purify and crystallize in large quantities. This work demonstrates a scheme to encapsulate biological samples using polymer thin films and graphene to maintain sample hydration in vacuum conditions. The encapsulated sample is delivered into the X-ray beam on fixed targets for rapid scanning using the Roadrunner fixed-target system towards a long-term goal of low-background measurements on weakly diffracting samples. As a proof of principle, we used microcrystals of the 24 kDa rapid encystment protein (REP24) to provide a benchmark for polymer/graphene sandwich performance. The REP24 microcrystal unit cell obtained from our sandwiched in-vacuum sample was consistent with previously established unit-cell parameters and with those measured by us without encapsulation in humidified helium, indicating that the platform is robust against evaporative losses. While significant scattering from water was observed because of the sample-deposition method, the polymer/graphene sandwich itself was shown to contribute minimally to background scattering.

Virus Structures by X-Ray Free-Electron Lasers

Until recently X-ray crystallography has been the standard technique for virus structure determinations. Available X-ray sources have continuously improved over the decades, leading to the realization of X-ray free-electron lasers (XFELs). They provide high-intensity femtosecond X-ray pulses, which allow for new kinds of experiments by making use of the diffraction-before-destruction principle. By overcoming classical dose constraints, they at least in principle allow researchers to perform X-ray virus structure determination for single particles at room temperature. Simultaneously, the availability of XFELs led to the development of the method of serial femtosecond crystallography, where a crystal structure is determined from the measurement of hundreds to thousands of microcrystals. In the case of virus crystallography this method does not require freezing of the crystals and allows researchers to perform experiments under non-equilibrium conditions (e.g., by laser-induced temperature jumps or rapid chemical mixing), which is currently not possible with electron microscopy.

1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector

Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s.

A DuMond-type crystal spectrometer for synchrotron-based X-ray emission studies in the energy range of 15-26 keV

The design and performance of a high-resolution transmission-type X-ray spectrometer for use in the 15-26 keV energy range at synchrotron light sources is reported. Monte Carlo X-ray-tracing simulations were performed to optimize the performance of the transmission-type spectrometer, based on the DuMond geometry, for use at the Super X-ray absorption beamline of the Swiss Light Source at the Paul Scherrer Institute. This spectrometer provides an instrumental energy resolution of 3.5 eV for X-ray emission lines around 16 keV and 12.5 eV for emission lines at 26 keV, which is comparable to the natural linewidths of the K and L X-ray transitions in the covered energy range. First experimental data are presented and compared with results of the Monte Carlo X-ray simulations.

Femtosecond phase-transition in hard x-ray excited bismuth

The evolution of bismuth crystal structure upon excitation of its A_1g phonon has been intensely studied with short pulse optical lasers. Here we present the first-time observation of a hard x-ray induced ultrafast phase transition in a bismuth single crystal at high intensities (~10¹⁴ W/cm²). The lattice evolution was followed using a recently demonstrated x-ray single-shot probing setup. The time evolution of the (111) Bragg peak intensity showed strong dependence on the excitation fluence. After exposure to a sufficiently intense x-ray pulse, the peak intensity dropped to zero within 300 fs, i.e. faster than one oscillation period of the A_1g mode at room temperature. Our analysis indicates a nonthermal origin of a lattice disordering process, and excludes interpretations based on electron-ion equilibration process, or on thermodynamic heating process leading to plasma formation.

Pink-beam serial crystallography

Serial X-ray crystallography allows macromolecular structure determination at both X-ray free electron lasers (XFELs) and, more recently, synchrotron sources. The time resolution for serial synchrotron crystallography experiments has been limited to millisecond timescales with monochromatic beams. The polychromatic, "pink", beam provides a more than two orders of magnitude increased photon flux and hence allows accessing much shorter timescales in diffraction experiments at synchrotron sources. Here we report the structure determination of two different protein samples by merging pink-beam diffraction patterns from many crystals, each collected with a single 100 ps X-ray pulse exposure per crystal using a setup optimized for very low scattering background. In contrast to experiments with monochromatic radiation, data from only 50 crystals were required to obtain complete datasets. The high quality of the diffraction data highlights the potential of this method for studying irreversible reactions at sub-microsecond timescales using high-brightness X-ray facilities.

AXSIS: Exploring the frontiers in attosecond X-ray science, imaging and spectroscopy

X-ray crystallography is one of the main methods to determine atomic-resolution 3D images of the whole spectrum of molecules ranging from small inorganic clusters to large protein complexes consisting of hundred-thousands of atoms that constitute the macromolecular machinery of life. Life is not static, and unravelling the structure and dynamics of the most important reactions in chemistry and biology is essential to uncover their mechanism. Many of these reactions, including photosynthesis which drives our biosphere, are light induced and occur on ultrafast timescales. These have been studied with high time resolution primarily by optical spectroscopy, enabled by ultrafast laser technology, but they reduce the vast complexity of the process to a few reaction coordinates. In the AXSIS project at CFEL in Hamburg, funded by the European Research Council, we develop the new method of attosecond serial X-ray crystallography and spectroscopy, to give a full description of ultrafast processes atomically resolved in real space and on the electronic energy landscape, from co-measurement of X-ray and optical spectra, and X-ray diffraction. This technique will revolutionize our understanding of structure and function at the atomic and molecular level and thereby unravel fundamental processes in chemistry and biology like energy conversion processes. For that purpose, we develop a compact, fully coherent, THz-driven atto-second X-ray source based on coherent inverse Compton scattering off a free-electron crystal, to outrun radiation damage effects due to the necessary high X-ray irradiance required to acquire diffraction signals. This highly synergistic project starts from a completely clean slate rather than conforming to the specifications of a large free-electron laser (FEL) user facility, to optimize the entire instrumentation towards fundamental measurements of the mechanism of light absorption and excitation energy transfer. A multidisciplinary team formed by laser-, accelerator,- X-ray scientists as well as spectroscopists and biochemists optimizes X-ray pulse parameters, in tandem with sample delivery, crystal size, and advanced X-ray detectors. Ultimately, the new capability, attosecond serial X-ray crystallography and spectroscopy, will be applied to one of the most important problems in structural biology, which is to elucidate the dynamics of light reactions, electron transfer and protein structure in photosynthesis.

Time-resolved pump and probe x-ray absorption fine structure spectroscopy at beamline P11 at PETRA III

We report about the development and implementation of a new setup for time-resolved X-ray absorption fine structure spectroscopy at beamline P11 utilizing the outstanding source properties of the low-emittance PETRA III synchrotron storage ring in Hamburg. Using a high intensity micrometer-sized X-ray beam in combination with two positional feedback systems, measurements were performed on the transition metal complex fac-Tris[2-phenylpyridinato-C2,N]iridium(III) also referred to as fac-Ir(ppy)3. This compound is a representative of the phosphorescent iridium(III) complexes, which play an important role in organic light emitting diode (OLED) technology. The experiment could directly prove the anticipated photoinduced charge transfer reaction. Our results further reveal that the temporal resolution of the experiment is limited by the PETRA III X-ray bunch length of ∼103 ps full width at half maximum (FWHM).

Charge-density studies of energetic materials: CL-20 and FOX-7. Corrigendum

A corrigendum to the paper by Meents et al. (2008), Acta Cryst. B64, 42–49 to correct the nomenclature for CL-20.

Charge-density studies of energetic materials: CL-20 and FOX-7

Experimental electron densities and derived properties have been determined for the two energetic materials CL-20 (3,5,9,11-tetraacetyl-14-oxo-1,3,5,7,9,11-hexaazapentacyclo-[5.5.3.02,6.04,10.08,12]pentadecane), and FOX-7 (1,1-diamino-2,2-dinitroethylene) from single-crystal diffraction. Synchrotron data extending to high scattering angles were measured at low temperature. Low figures-of-merit and excellent residuals were obtained. The Hansen & Coppens multipole-model electron density was compared with results from theoretical calculations via structure factors simulating an experiment. Chemical bonding in the molecules is discussed and a topological analysis gives insight especially into the character of those bonds that are thought to play a key role in the decomposition of the molecules. A comparison of theoretical and experimental electrostatic potentials shows no obvious evidence supporting earlier findings on other nitroheterocyclic molecules that electron-density maxima near the C-NO(2) bonds mapped on the electron-density isosurface can be correlated with impact sensitivities. For FOX-7 periodic Hartree-Fock calculations were performed to investigate the influence of the crystal field on the electron density distribution.

Using X-ray absorption spectra to monitor specific radiation damage to anomalously scattering atoms in macromolecular crystallography

Radiation damage in macromolecular crystals is not suppressed even at 90 K. This is particularly true for covalent bonds involving an anomalous scatterer (such as bromine) at the 'peak wavelength'. It is shown that a series of absorption spectra recorded on a brominated RNA faithfully monitor the extent of cleavage. The continuous spectral changes during irradiation preserve an 'isosbestic point', each spectrum being a linear combination of 'zero' and 'infinite' dose spectra. This easily yields a good estimate of the partial occupancy of bromine at any intermediate dose. The considerable effect on the near-edge features in the spectra of the crystal orientation versus the beam polarization has also been examined and found to be in good agreement with a previous study. Any significant influence of the (C-Br bond/beam polarization) angle on the cleavage kinetics of bromine was also searched for, but was not detected. These results will be useful for standard SAD/MAD experiments and for the emerging 'radiation-damage-induced phasing' method exploiting both the anomalous signal of an anomalous scatterer and the 'isomorphous' signal resulting from its cleavage.

Reduction of X-ray-induced radiation damage of macromolecular crystals by data collection at 15 K: a systematic study

The cryocooling of protein crystals to temperatures of around 100 K drastically reduces X-ray-induced radiation damage. The majority of macromolecular data collection is therefore performed at 100 K, yielding diffraction data of higher resolution and allowing structure determination from much smaller crystals. However, at third-generation synchrotron sources radiation damage at 100 K still limits the useful data obtainable from a crystal. For data collection at 15 K, realised by the use of an open-flow helium cryostat, a further reduction of radiation damage is expected. However, no systematic studies have been undertaken so far. In this present study, a total of 54 data sets have been collected from holoferritin and insulin crystals at 15 and 90 K in order to identify the effect of the lower data-collection temperature on the radiation damage. It is shown that data collection at 15 K has only a small positive effect for insulin crystals, whereas for holoferritin crystals radiation damage is reduced by 23% compared with data collection at 90 K.

Crystal structure of Tutton’s salts, Cs2[MII(H2O)6](SO4)2, MII = Mg, Mn, Fe, Co, Ni, Zn

Cs2H12MgO14S2, monoclinic, P121/a1 (No. 14), a = 9.338(2) Å, b = 12.849(4) Å, c = 6.361(2) Å, β = 107.07(2)°, V = 729.6 Å3, Z = 2, Rgt(F) = 0.017, wRref(F2) = 0.041, T = 293 K.

Cs2H12MnO14S2, monoclinic, P121/a1 (No. 14), a = 9.418(3) Å, b = 12.963(2) Å, c = 6.386(3) Å, β = 107.17(4)°, V = 744.9 Å3, Z = 2, Rgt(F) = 0.017, wRref(F2) = 0.030, T = 293 K.

Cs2FeO14H12S2, monoclinic, P121/a1 (No. 14), a = 9.357(2) Å, b = 12.886(2) Å, c = 6.381(1) Å, β = 106.94(1)°, V = 736.0 Å3, Z = 2, Rgt(F) = 0.015, wRref(F2) = 0.030, T = 293 K.

CoCs2H12O14S2, monoclinic, P121/a1 (No. 14), a = 9.318(1) Å, b = 12.826(3) Å, c = 6.3650(9) Å, β = 107.13(1)°, V = 727.0 Å3, Z = 2, Rgt(F) = 0.021, wRref(F2) = 0.049, T = 293 K.

Cs2H12NiO14S2, monoclinic, P121/a1 (No. 14), a = 9.259(2) Å, b = 12.767(2) Å, c = 6.358(1) Å, β = 107.00(2)°, V = 718.7 Å3, Z = 2, Rgt(F) = 0.014, wRref(F2) = 0.027, T = 293 K.

Cs2H12O14S2Zn, monoclinic, P121/a1 (No. 14), a = 9.314(2) Å, b = 12.817(2) Å, c = 6.369(2) Å, β = 106.94(2)°, V = 727.3 Å3, Z = 2, Rgt(F) = 0.015, wRref(F2) = 0.033, T = 293 K.

Crystal structure of Tutton’s salts, Cs2[MII(H2O)6](SeO4)2, MII = Mg, Mn, Co, Ni, Zn

Cs2H12MgO14Se2, monoclinic, P121/a1 (No. 14), a = 9.513(1) Å, b = 13.037(1) Å, c = 6.4730(8) Å, β = 106.244(8)°, V = 770.7 Å3, Z = 2, Rgt(F) = 0.020, wRref(F2) = 0.036, T = 293 K.

Cs2H12MnO14Se2, monoclinic, P121/a1 (No. 14), a = 9.591(1) Å, b = 13.141(2) Å, c = 6.5040(9) Å, β = 106.38(1)°, V = 786.5 Å3, Z = 2, Rgt(F) = 0.021, wRref(F2) = 0.043, T = 293 K.

CoCs2H12O14Se2, monoclinic, P121/a1 (No. 14), a = 9.494(1)Å, b = 13.009(1) Å, c = 6.4833(8) Å, β = 106.239(9)°, V = 768.8 Å3, Z = 2, Rgt(F) = 0.016, wRref(F2) = 0.032, T = 293 K.

Cs2H12NiO14Se2, monoclinic, P121/a1 (No. 14), a = 9.426(3)Å, b = 12.961(2) Å, c = 6.473(2) Å, β = 106.17(2)°, V = 759.5 Å3, Z = 2, Rgt(F) = 0.017, wRref(F2) = 0.034, T = 293 K.

Cs2H12O14Se2Zn, monoclinic, P121/a1 (No. 14), a = 9.483(1) Å, b = 13.005(2) Å, c = 6.4850(8) Å, β = 106.16(1)°, V = 768.2 Å3, Z = 2, Rgt(F) = 0.019, wRref(F2) = 0.037, T = 293 K.

Crystal structure of Tutton’s salts, Rb2[MII(H2O)6](SeO4)2, MII = Mg, Co, Mn, Zn

H12MgO14Rb2Se2, monoclinic, P121/a1 (No. 14), a = 9.401(1) Å, b = 12.658(2) Å, c = 6.339(1) Å, β = 105.25(1)°, V = 727.8 Å3, Z = 2, Rgt(F) = 0.020, wRref(F2) = 0.040, T = 293 K.

CoH12O14Rb2Se2, monoclinic, P121/a1 (No. 14), a = 9.363(1) Å, b = 12.618(1) Å, c = 6.3562(7) Å, β = 105.238(9)°, V = 724.5Å3, Z = 2, Rgt(F) = 0.018, wRref(F2) = 0.037, T = 293 K.

H12MnO14Rb2Se2, monoclinic, P121/a1 (No. 14), a = 9.4496(8) Å, b = 12.760(1) Å, c = 6.3794(7) Å, β = 105.189(7)°, V = 742.4Å3, Z = 2, Rgt(F) = 0.025, wRref(F2) = 0.056, T = 293 K.

H12O14Rb2Se2Zn, monoclinic, P121/a1 (No. 14), a = 9.352(1) Å, b = 12.626(2) Å, c = 6.360(1) Å, β = 105.195(8)°, V = 724.7 Å3, Z = 2, Rgt(F) = 0.024, wRref(F2) = 0.048, T = 293 K.