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1.  Femtosecond X-ray protein nanocrystallography 
Chapman, Henry N. | Fromme, Petra | Barty, Anton | White, Thomas A. | Kirian, Richard A. | Aquila, Andrew | Hunter, Mark S. | Schulz, Joachim | DePonte, Daniel P. | Weierstall, Uwe | Doak, R. Bruce | Maia, Filipe R. N. C. | Martin, Andrew V. | Schlichting, Ilme | Lomb, Lukas | Coppola, Nicola | Shoeman, Robert L. | Epp, Sascha W. | Hartmann, Robert | Rolles, Daniel | Rudenko, Artem | Foucar, Lutz | Kimmel, Nils | Weidenspointner, Georg | Holl, Peter | Liang, Mengning | Barthelmess, Miriam | Caleman, Carl | Boutet, Sébastien | Bogan, Michael J. | Krzywinski, Jacek | Bostedt, Christoph | Bajt, Saša | Gumprecht, Lars | Rudek, Benedikt | Erk, Benjamin | Schmidt, Carlo | Hömke, André | Reich, Christian | Pietschner, Daniel | Strüder, Lothar | Hauser, Günter | Gorke, Hubert | Ullrich, Joachim | Herrmann, Sven | Schaller, Gerhard | Schopper, Florian | Soltau, Heike | Kühnel, Kai-Uwe | Messerschmidt, Marc | Bozek, John D. | Hau-Riege, Stefan P. | Frank, Matthias | Hampton, Christina Y. | Sierra, Raymond G. | Starodub, Dmitri | Williams, Garth J. | Hajdu, Janos | Timneanu, Nicusor | Seibert, M. Marvin | Andreasson, Jakob | Rocker, Andrea | Jönsson, Olof | Svenda, Martin | Stern, Stephan | Nass, Karol | Andritschke, Robert | Schröter, Claus-Dieter | Krasniqi, Faton | Bott, Mario | Schmidt, Kevin E. | Wang, Xiaoyu | Grotjohann, Ingo | Holton, James M. | Barends, Thomas R. M. | Neutze, Richard | Marchesini, Stefano | Fromme, Raimund | Schorb, Sebastian | Rupp, Daniela | Adolph, Marcus | Gorkhover, Tais | Andersson, Inger | Hirsemann, Helmut | Potdevin, Guillaume | Graafsma, Heinz | Nilsson, Björn | Spence, John C. H.
Nature  2011;470(7332):73-77.
X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded1-3. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction ‘snapshots’ are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source4. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes5. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (~200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes6. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
doi:10.1038/nature09750
PMCID: PMC3429598  PMID: 21293373
2.  Time-resolved protein nanocrystallography using an X-ray free-electron laser 
Aquila, Andrew | Hunter, Mark S | Bruce Doak, R. | Kirian, Richard A. | Fromme, Petra | White, Thomas A. | Andreasson, Jakob | Arnlund, David | Bajt, Saša | Barends, Thomas R. M. | Barthelmess, Miriam | Bogan, Michael J. | Bostedt, Christoph | Bottin, Hervé | Bozek, John D. | Caleman, Carl | Coppola, Nicola | Davidsson, Jan | DePonte, Daniel P. | Elser, Veit | Epp, Sascha W. | Erk, Benjamin | Fleckenstein, Holger | Foucar, Lutz | Frank, Matthias | Fromme, Raimund | Graafsma, Heinz | Grotjohann, Ingo | Gumprecht, Lars | Hajdu, Janos | Hampton, Christina Y. | Hartmann, Andreas | Hartmann, Robert | Hau-Riege, Stefan | Hauser, Günter | Hirsemann, Helmut | Holl, Peter | Holton, James M. | Hömke, André | Johansson, Linda | Kimmel, Nils | Kassemeyer, Stephan | Krasniqi, Faton | Kühnel, Kai-Uwe | Liang, Mengning | Lomb, Lukas | Malmerberg, Erik | Marchesini, Stefano | Martin, Andrew V. | Maia, Filipe R.N.C. | Messerschmidt, Marc | Nass, Karol | Reich, Christian | Neutze, Richard | Rolles, Daniel | Rudek, Benedikt | Rudenko, Artem | Schlichting, Ilme | Schmidt, Carlo | Schmidt, Kevin E. | Schulz, Joachim | Seibert, M. Marvin | Shoeman, Robert L. | Sierra, Raymond | Soltau, Heike | Starodub, Dmitri | Stellato, Francesco | Stern, Stephan | Strüder, Lothar | Timneanu, Nicusor | Ullrich, Joachim | Wang, Xiaoyu | Williams, Garth J. | Weidenspointner, Georg | Weierstall, Uwe | Wunderer, Cornelia | Barty, Anton | Spence, John C. H | Chapman, Henry N.
Optics express  2012;20(3):2706-2716.
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 μs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
PMCID: PMC3413412  PMID: 22330507
3.  Time-resolved protein nanocrystallography using an X-ray free-electron laser 
Aquila, Andrew | Hunter, Mark S. | Doak, R. Bruce | Kirian, Richard A. | Fromme, Petra | White, Thomas A. | Andreasson, Jakob | Arnlund, David | Bajt, Saša | Barends, Thomas R. M. | Barthelmess, Miriam | Bogan, Michael J. | Bostedt, Christoph | Bottin, Hervé | Bozek, John D. | Caleman, Carl | Coppola, Nicola | Davidsson, Jan | DePonte, Daniel P. | Elser, Veit | Epp, Sascha W. | Erk, Benjamin | Fleckenstein, Holger | Foucar, Lutz | Frank, Matthias | Fromme, Raimund | Graafsma, Heinz | Grotjohann, Ingo | Gumprecht, Lars | Hajdu, Janos | Hampton, Christina Y. | Hartmann, Andreas | Hartmann, Robert | Hau-Riege, Stefan | Hauser, Günter | Hirsemann, Helmut | Holl, Peter | Holton, James M. | Hömke, André | Johansson, Linda | Kimmel, Nils | Kassemeyer, Stephan | Krasniqi, Faton | Kühnel, Kai-Uwe | Liang, Mengning | Lomb, Lukas | Malmerberg, Erik | Marchesini, Stefano | Martin, Andrew V. | Maia, Filipe R.N.C. | Messerschmidt, Marc | Nass, Karol | Reich, Christian | Neutze, Richard | Rolles, Daniel | Rudek, Benedikt | Rudenko, Artem | Schlichting, Ilme | Schmidt, Carlo | Schmidt, Kevin E. | Schulz, Joachim | Seibert, M. Marvin | Shoeman, Robert L. | Sierra, Raymond | Soltau, Heike | Starodub, Dmitri | Stellato, Francesco | Stern, Stephan | Strüder, Lothar | Timneanu, Nicusor | Ullrich, Joachim | Wang, Xiaoyu | Williams, Garth J. | Weidenspointner, Georg | Weierstall, Uwe | Wunderer, Cornelia | Barty, Anton | Spence, John C. H. | Chapman, Henry N.
Optics Express  2012;20(3):2706-2716.
We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin. The undocking process that follows the electron transfer leads to large rearrangements in the crystals that will terminally lead to the disintegration of the crystals. We describe the experimental setup and obtain the first time-resolved femtosecond serial X-ray crystallography results from an irreversible photo-chemical reaction at the Linac Coherent Light Source. This technique opens the door to time-resolved structural studies of reaction dynamics in biological systems.
doi:10.1364/OE.20.002706
PMCID: PMC3413412  PMID: 22330507
(170.7160) Ultrafast technology; (170.7440) X-ray imaging; (140.3450) Laser-induced chemistry; (140.7090) Ultrafast lasers; (170.0170) Medical optics and biotechnology
4.  Toward structure determination using membrane-protein nanocrystals and microcrystals 
Methods (San Diego, Calif.)  2011;55(4):387-404.
Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only a hundred unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet brought fully-hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses (~ 70 fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. During the initial experiments at the AMO beamline using 6.9-Å wavelength, Bragg peaks were recorded to 8.5-Å resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage [Chapman H.N., et al. Femtosecond X-ray protein nanocrystallography, Nature 470 (2011) 73–81]. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.
doi:10.1016/j.ymeth.2011.12.006
PMCID: PMC3414265  PMID: 22197730
membrane proteins; structure determination; femtosecond nanocrystallography; protein nanocrystals; X-ray crystallography; XFEL
5.  Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser 
X-ray free-electron lasers deliver intense femtosecond pulses that promise to yield high resolution diffraction data of nanocrystals before the destruction of the sample by radiation damage. Diffraction intensities of lysozyme nanocrystals collected at the Linac Coherent Light Source using 2 keV photons were used for structure determination by molecular replacement and analyzed for radiation damage as a function of pulse length and fluence. Signatures of radiation damage are observed for pulses as short as 70 fs. Parametric scaling used in conventional crystallography does not account for the observed effects.
doi:10.1103/PhysRevB.84.214111
PMCID: PMC3786679  PMID: 24089594
6.  Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature 
Science (New York, N.Y.)  2013;340(6131):491-495.
Intense femtosecond X-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous X-ray diffraction (XRD) and X-ray emission spectroscopy (XES) of microcrystals of Photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn4CaO5 cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S1) and the first illuminated state (S2) of PS II. Our simultaneous XRD/XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation sensitive Mn4CaO5 cluster, opening new directions for future dynamics studies.
doi:10.1126/science.1234273
PMCID: PMC3732582  PMID: 23413188
7.  High-resolution X-ray microdiffraction analysis of natural teeth 
Journal of Synchrotron Radiation  2008;15(Pt 3):235-238.
In situ microzone X-ray diffraction analysis of natural teeth is presented. From our experiment, layer orientation and continuous crystal variations in teeth could be conveniently studied using fast online measurements by high-resolution X-ray microdiffraction equipment.
The main component of natural teeth was determined many years ago as calcium phosphate, mostly in the form of hydroxyapatite with different crystallites. In the past, the method used in tooth crystal investigation has been mainly powder X-ray diffraction analysis, but this method has its drawbacks, i.e. the destruction of the natural tooth structure and the difficulty in examining the preferred orientation in different layers of the tooth. During the last century, microzone X-ray diffraction on the tooth surface was carried out, but, as the technology was less sophisticated, the results obtained were not very detailed. The newly developed microdiffraction equipment permits analysis of the microzone of teeth in situ. To test this new microdiffraction equipment, microdiffraction analysis of one natural healthy deciduous molar tooth and one carious deciduous molar tooth has been performed, using a Bruker D8 instrument. Phase analysis of the two teeth was performed; the crystal size at six test points in the natural healthy tooth was calculated by reflection (211), and the crystal preferred orientation of reflection (300) and reflection (002) at six test points in the natural healthy tooth were compared. The results showed that the tooth was a kind of biological mixed crystal composed of several crystal phases, the main crystal phase being hydroxyapatite. The crystal size grew larger going from the dentin to the enamel. The crystal preferred orientation mainly existed in the enamel, especially in the reflection (002). From our experiment, layer orientation and continuous crystal variations in teeth could be conveniently studied using fast online measurements by high-resolution X-ray microdiffraction equipment.
doi:10.1107/S0909049508003397
PMCID: PMC2394821  PMID: 18421147
X-ray microdiffraction; enamel; caries; texture; crystal
8.  Unit-cell determination from randomly oriented electron-diffraction patterns 
An algorithm is described that calculates the most likely primitive unit cell given a set of randomly oriented electron-diffraction patterns with unknown angular relationships.
Unit-cell determination is the first step towards the structure solution of an unknown crystal form. Standard procedures for unit-cell determination cannot cope with data collections that consist of single diffraction patterns of multiple crystals, each with an unknown orientation. However, for beam-sensitive nanocrystals these are often the only data that can be obtained. An algorithm for unit-cell determination that uses randomly oriented electron-diffraction patterns with unknown angular relationships is presented here. The algorithm determined the unit cells of mineral, pharmaceutical and protein nanocrystals in orthorhombic high- and low-symmetry space groups, allowing (well oriented) patterns to be indexed.
doi:10.1107/S0907444909003163
PMCID: PMC2703568  PMID: 19564682
electron diffraction; nanocrystals; unit-cell determination; unknown orientation
9.  Emerging opportunities in structural biology with X-ray free-electron lasers 
X-ray free-electron lasers (X-FELs) produce X-ray pulses with extremely brilliant peak intensity and ultrashort pulse duration. It has been proposed that radiation damage can be “outrun” by using an ultra intense and short X-FEL pulse that passes a biological sample before the onset of significant radiation damage. The concept of “diffraction-before-destruction” has been demonstrated recently at the Linac Coherent Light Source, the first operational hard X-ray FEL, for protein nanocrystals and giant virus particles. The continuous diffraction patterns from single particles allow solving the classical “phase problem” by the oversampling method with iterative algorithms. If enough data are collected from many identical copies of a (biological) particle, its three-dimensional structure can be reconstructed. We review the current status and future prospects of serial femtosecond crystallography (SFX) and single-particle coherent diffraction imaging (CDI) with X-FELs.
doi:10.1016/j.sbi.2012.07.015
PMCID: PMC3495068  PMID: 22922042
10.  Evolution of long-range myofibrillar crystallinity in insect flight muscle as examined by X-ray cryomicrodiffraction 
Insect flight muscle is known for its crystal-quality regularity of contractile protein arrangement within a sarcomere. We have previously shown by X-ray microdiffraction that the crystal-quality regularity in bumble-bee flight muscle is not confined within a sarcomere, but extends over the entire length of a myofibril (>1000 sarcomeres connected in series). Because of this, the whole myofibril may be regarded as a millimetre-long, natural single protein crystal. Using bright X-ray beams from a synchrotron radiation source, we examined how this long-range crystallinity has evolved among winged insects. We analysed >4600 microdiffraction patterns of quick-frozen myofibrils from 50 insect species, covering all the major winged insect orders. The results show that the occurrence of such long-range crystallinity largely coincides with insect orders with asynchronous muscle operation. However, a few of the more skilled fliers among lower-order insects apparently have developed various degrees of structural regularity, suggesting that the demand for skilful flight has driven the lattice structure towards increased regularity.
doi:10.1098/rspb.2005.3389
PMCID: PMC1560076  PMID: 16608686
synchrotron radiation; microbeam; single myofibril; single sarcomere; liquid-nitrogen temperature
11.  Tunable Visible Emission of Ag-Doped CdZnS Alloy Quantum Dots 
Nanoscale Research Letters  2009;5(1):96-102.
Highly luminescent Ag-ion-doped Cd1−xZnxS (0 ≤ x ≤ 1) alloy nanocrystals were successfully synthesized by a novel wet chemical precipitation method. Influence of dopant concentration and the Zn/Cd stoichiometric variations in doped alloy nanocrystals have been investigated. The samples were characterized by X-ray diffraction (XRD) and high resolution transmission electron microscope (HRTEM) to investigate the size and structure of the as prepared nanocrystals. A shift in LO phonon modes from micro-Raman investigations and the elemental analysis from the energy dispersive X-ray analysis (EDAX) confirms the stoichiometry of the final product. The average crystallite size was found increasing from 1.0 to 1.4 nm with gradual increase in Ag doping. It was observed that photoluminescence (PL) intensity corresponding to Ag impurity (570 nm), relative to the other two bands 480 and 520 nm that originates due to native defects, enhanced and showed slight red shift with increasing silver doping. In addition, decrease in the band gap energy of the doped nanocrystals indicates that the introduction of dopant ion in the host material influence the particle size of the nanocrystals. The composition dependent bandgap engineering in CdZnS:Ag was achieved to attain the deliberate color tunability and demonstrated successfully, which are potentially important for white light generation.
doi:10.1007/s11671-009-9449-9
PMCID: PMC2893933  PMID: 20652135
Alloy; Nanocrystals; Photoluminescence; Raman spectroscopy
12.  Tunable Visible Emission of Ag-Doped CdZnS Alloy Quantum Dots 
Nanoscale Research Letters  2009;5(1):96-102.
Highly luminescent Ag-ion-doped Cd1−xZnxS (0 ≤ x ≤ 1) alloy nanocrystals were successfully synthesized by a novel wet chemical precipitation method. Influence of dopant concentration and the Zn/Cd stoichiometric variations in doped alloy nanocrystals have been investigated. The samples were characterized by X-ray diffraction (XRD) and high resolution transmission electron microscope (HRTEM) to investigate the size and structure of the as prepared nanocrystals. A shift in LO phonon modes from micro-Raman investigations and the elemental analysis from the energy dispersive X-ray analysis (EDAX) confirms the stoichiometry of the final product. The average crystallite size was found increasing from 1.0 to 1.4 nm with gradual increase in Ag doping. It was observed that photoluminescence (PL) intensity corresponding to Ag impurity (570 nm), relative to the other two bands 480 and 520 nm that originates due to native defects, enhanced and showed slight red shift with increasing silver doping. In addition, decrease in the band gap energy of the doped nanocrystals indicates that the introduction of dopant ion in the host material influence the particle size of the nanocrystals. The composition dependent bandgap engineering in CdZnS:Ag was achieved to attain the deliberate color tunability and demonstrated successfully, which are potentially important for white light generation.
doi:10.1007/s11671-009-9449-9
PMCID: PMC2893933  PMID: 20652135
Alloy; Nanocrystals; Photoluminescence; Raman spectroscopy
13.  Discrete plasticity in sub-10-nm-sized gold crystals 
Nature Communications  2010;1:144-.
Although deformation processes in submicron-sized metallic crystals are well documented, the direct observation of deformation mechanisms in crystals with dimensions below the sub-10-nm range is currently lacking. Here, through in situ high-resolution transmission electron microscopy (HRTEM) observations, we show that (1) in sharp contrast to what happens in bulk materials, in which plasticity is mediated by dislocation emission from Frank-Read sources and multiplication, partial dislocations emitted from free surfaces dominate the deformation of gold (Au) nanocrystals; (2) the crystallographic orientation (Schmid factor) is not the only factor in determining the deformation mechanism of nanometre-sized Au; and (3) the Au nanocrystal exhibits a phase transformation from a face-centered cubic to a body-centered tetragonal structure after failure. These findings provide direct experimental evidence for the vast amount of theoretical modelling on the deformation mechanisms of nanomaterials that have appeared in recent years.
Deformations in nanocrystals smaller than 10 nm are not well understood. The authors perform compression high-resolution transmission electron microscopy studies of gold nanoparticles, and determine that the nanoparticles deform through the emission of partial dislocations from free surfaces.
doi:10.1038/ncomms1149
PMCID: PMC3105591  PMID: 21266994
14.  Nanoflow electrospinning serial femtosecond crystallography 
A low flow rate liquid microjet method for delivery of hydrated protein crystals to X-ray lasers is presented. Linac Coherent Light Source data demonstrates serial femtosecond protein crystallography with micrograms, a reduction of sample consumption by orders of magnitude.
An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14–3.1 µl min−1 to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 µl min−1 and diffracted to beyond 4 Å resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 µg of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.
doi:10.1107/S0907444912038152
PMCID: PMC3478121  PMID: 23090408
serial femtosecond crystallography; nanoflow electrospinning
15.  Femtosecond nanocrystallography using X-Ray Lasers for membrane protein structure determination 
The invention of Free Electron X-ray Lasers has opened a new era for membrane protein structure determination with the recent first proof-of-principle of the new concept of femtosecond nanocrystallography. Structure determination is based on thousands of diffraction snapshots that are collected on a fully hydrated stream of nanocrystals. This review provides a summary of the method and describes how femtosecond X-ray crystallography overcomes the radiation damage problem in X-ray crystallography, avoids the need for growth and freezing of large single crystals while offering a new method for direct digital phase determination by making use of the fully coherent nature of the X-ray beam. We briefly review the possibilities for time-resolved crystallography, and the potential for making “molecular movies” of membrane proteins at work.
doi:10.1016/j.sbi.2011.06.001
PMCID: PMC3413407  PMID: 21752635
16.  A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals 
An ultrasensitive Medipix2 detector allowed the collection of rotation electron-diffraction data from single three-dimensional protein nanocrystals for the first time. The data could be analysed using the standard X-ray crystallography programs MOSFLM and SCALA.
When protein crystals are submicrometre-sized, X-ray radiation damage precludes conventional diffraction data collection. For crystals that are of the order of 100 nm in size, at best only single-shot diffraction patterns can be collected and rotation data collection has not been possible, irrespective of the diffraction technique used. Here, it is shown that at a very low electron dose (at most 0.1 e− Å−2), a Medipix2 quantum area detector is sufficiently sensitive to allow the collection of a 30-frame rotation series of 200 keV electron-diffraction data from a single ∼100 nm thick protein crystal. A highly parallel 200 keV electron beam (λ = 0.025 Å) allowed observation of the curvature of the Ewald sphere at low resolution, indicating a combined mosaic spread/beam divergence of at most 0.4°. This result shows that volumes of crystal with low mosaicity can be pinpointed in electron diffraction. It is also shown that strategies and data-analysis software (MOSFLM and SCALA) from X-ray protein crystallography can be used in principle for analysing electron-diffraction data from three-dimensional nanocrystals of proteins.
doi:10.1107/S0907444913009700
PMCID: PMC3689525  PMID: 23793148
electron diffraction; electron microscopy; Medipix2; MOSFLM; nanocrystals
17.  Structure of a photosynthetic reaction centre determined by serial femtosecond crystallography 
Nature Communications  2013;4:2911.
Serial femtosecond crystallography is an X-ray free-electron-laser-based method with considerable potential to have an impact on challenging problems in structural biology. Here we present X-ray diffraction data recorded from microcrystals of the Blastochloris viridis photosynthetic reaction centre to 2.8 Å resolution and determine its serial femtosecond crystallography structure to 3.5 Å resolution. Although every microcrystal is exposed to a dose of 33 MGy, no signs of X-ray-induced radiation damage are visible in this integral membrane protein structure.
Serial femtosecond crystallography is an X-ray free-electron-laser-based method that uses X-ray bursts to determine protein structures. Here the authors present the structure of a photosynthetic reaction centre, an integral membrane protein, achieved with no sign of X-ray-induced radiation damage.
doi:10.1038/ncomms3911
PMCID: PMC3905732  PMID: 24352554
18.  Structural, spectroscopic and cytotoxicity studies of TbF3@CeF3 and TbF3@CeF3@SiO2 nanocrystals 
Abstract
Terbium fluoride nanocrystals, covered by a shell, composed of cerium fluoride were synthesized by a co-precipitation method. Their complex structure was formed spontaneously during the synthesis. The surface of these core/shell nanocrystals was additionally modified by silica. The properties of TbF3@CeF3 and TbF3@CeF3@SiO2 nanocrystals, formed in this way, were investigated. Spectroscopic studies showed that the differences between these two groups of products resulted from the presence of the SiO2 shell. X-ray diffraction patterns confirmed the trigonal crystal structure of TbF3@CeF3 nanocrystals. High resolution transmission electron microscopy in connection with energy-dispersive X-ray spectroscopy showed a complex structure of the formed nanocrystals. Crystallized as small discs, ‘the products’, with an average diameter around 10 nm, showed an increase in the concentration of Tb3+ ions from surface to the core of nanocrystals. In addition to photo-physical analyses, cytotoxicity studies were performed on HSkMEC (Human Skin Microvascular Endothelial Cells) and B16F0 mouse melanoma cancer cells. The cytotoxicity of the nanomaterials was neutral for the investigated cells with no toxic or antiproliferative effect in the cell cultures, either for normal or for cancer cells. This fact makes the obtained nanocrystals good candidates for biological applications and further modifications of the SiO2 shell.
Graphical Abstract
.
doi:10.1007/s11051-013-1958-x
PMCID: PMC3825480  PMID: 24273438
Nanoparticles; Core/shell; Silica; Luminescence; Rare earth fluorides; Cytotoxicity
19.  X-ray diffraction study of nanocrystalline and amorphous structure within major and minor ampullate dragline spider silks 
Soft matter  2012;8(25):6713-6722.
Synchrotron X-ray micro-diffraction experiments were carried out on Nephila clavipes (NC) and Argiope aurantia (AA) major (MA) and minor ampullate (MiA) fibers that make up dragline spider silk. The diffraction patterns show a semi-crystalline structure with β-poly(l-alanine) nanocrystallites embedded in a partially oriented amorphous matrix. A superlattice reflection ‘S’ diffraction ring is observed, which corresponds to a crystalline component larger in size and is poorly oriented, when compared to the β-poly(l-alanine) nanocrystallites that are commonly observed in dragline spider silks. Crystallite size, crystallinity and orientation about the fiber axis have been determined from the wide-angle X-ray diffraction (WAXD) patterns. In both NC and AA, the MiA silks are found to be more highly crystalline, when compared with the corresponding MA silks. Detailed analysis on the amorphous matrix shows considerable differences in the degree of order of the oriented amorphous component between the different silks studied and may play a crucial role in determining the mechanical properties of the silks.
doi:10.1039/C2SM25373A
PMCID: PMC3617558  PMID: 23569461
20.  Fast X-ray microdiffraction techniques for studying irreversible transformations in materials 
Journal of Synchrotron Radiation  2011;18(Pt 3):464-474.
Techniques are described for X-ray diffraction combining micrometer-scale spatial resolution with microsecond-scale temporal resolution for studying rapid localized irreversible transformations in materials.
A pair of techniques have been developed for performing time-resolved X-ray microdiffraction on irreversible phase transformations. In one technique capillary optics are used to focus a high-flux broad-spectrum X-ray beam to a 60 µm spot size and a fast pixel array detector is used to achieve temporal resolution of 55 µs. In the second technique the X-rays are focused with Kirkpatrick–Baez mirrors to achieve a spatial resolution better than 10 µm and a fast shutter is used to provide temporal resolution better than 20 µs while recording the diffraction pattern on a (relatively slow) X-ray CCD camera. Example data from experiments are presented where these techniques are used to study self-propagating high-temperature synthesis reactions in metal laminate foils.
doi:10.1107/S0909049511002640
PMCID: PMC3083916  PMID: 21525656
X-ray diffraction; phase transformations
21.  Bayesian algorithms for recovering structure from single-particle diffraction snapshots of unknown orientation: a comparison 
X-ray free-electron lasers are being used to determine the three-dimensional structure of objects from random snapshots. The two apparently very different Bayesian algorithms capable of performing this at ultra-low signal are fundamentally the same.
The advent of X-ray free-electron lasers promises the possibility to determine the structure of individual particles such as microcrystallites, viruses and biomolecules from single-shot diffraction snapshots obtained before the particle is destroyed by the intense femtosecond pulse. This program requires the ability to determine the orientation of the particle giving rise to each snapshot at signal levels as low as ~10−2 photons per pixel. Two apparently different approaches have recently demonstrated this capability. Here we show they represent different implementations of the same fundamental approach, and identify the primary factors limiting their performance.
doi:10.1107/S0108767311019611
PMCID: PMC3171899  PMID: 21844653
X-ray scattering; single-particle structure determination
22.  The Cost-Effectiveness of Improving Diabetes Care in U.S. Federally Qualified Community Health Centers 
Health Services Research  2007;42(6 Pt 1):2174-2193.
Objective
To estimate the incremental cost-effectiveness of improving diabetes care with the Health Disparities Collaborative (HDC), a national collaborative quality improvement (QI) program conducted in community health centers (HCs).
Data Sources/Study Setting
Data regarding the impact of the Diabetes HDC program came from a serial cross-sectional follow-up study (1998, 2000, 2002) of the program in 17 Midwestern HCs. Data inputs for the simulation model of diabetes came from the latest clinical trials and epidemiological studies.
Study Design
We conducted a societal cost-effectiveness analysis, incorporating data from QI program evaluation into a Monte Carlo simulation model of diabetes.
Data Collection/Extraction Methods
Data on diabetes care processes and risk factor levels were extracted from medical charts of randomly selected patients.
Principal Findings
From 1998 to 2002, multiple processes of care (e.g., glycosylated hemoglobin testing [HbA1C] [71→92 percent] and ACE inhibitor prescribing [33→55 percent]) and risk factor levels (e.g., 1998 mean HbA1C 8.53 percent, mean difference 0.45 percent [95 percent confidence intervals −0.72, −0.17]) improved significantly. With these improvements, the HDC was estimated to reduce the lifetime incidence of blindness (17→15 percent), end-stage renal disease (18→15 percent), and coronary artery disease (28→24 percent). The average improvement in quality-adjusted life year (QALY) was 0.35 and the incremental cost-effectiveness ratio was $33,386/QALY.
Conclusions
During the first 4 years of the HDC, multiple improvements in diabetes care were observed. If these improvements are maintained or enhanced over the lifetime of patients, the HDC program will be cost-effective for society based on traditionally accepted thresholds.
doi:10.1111/j.1475-6773.2007.00734.x
PMCID: PMC2151395  PMID: 17995559
Quality improvement; cost-effectiveness analysis; safety net providers
23.  The Cost-Effectiveness of Improving Diabetes Care in U.S. Federally Qualified Community Health Centers 
Health services research  2007;42(6 Pt 1):2174-2323.
Objective
To estimate the incremental cost-effectiveness of improving diabetes care with the Health Disparities Collaborative (HDC), a national collaborative quality improvement (QI) program conducted in community health centers (HCs).
Data Sources/Study Setting
Data regarding the impact of the Diabetes HDC program came from a serial cross-sectional follow-up study (1998, 2000, 2002) of the program in 17 Midwestern HCs. Data inputs for the simulation model of diabetes came from the latest clinical trials and epidemiological studies.
Study Design
We conducted a societal cost-effectiveness analysis, incorporating data from QI program evaluation into a Monte Carlo simulation model of diabetes.
Data Collection/Extraction Methods
Data on diabetes care processes and risk factor levels were extracted from medical charts of randomly selected patients.
Principal Findings
From 1998 to 2002, multiple processes of care (e.g., glycosylated hemoglobin testing [HbA1C] [71 → 92 percent] and ACE inhibitor prescribing [33 → 55 percent]) and risk factor levels (e.g., 1998 mean HbA1C 8.53 percent, mean difference 0.45 percent [95 percent confidence intervals −0.72, −0.17]) improved significantly. With these improvements, the HDC was estimated to reduce the lifetime incidence of blindness (17 → 15 percent), end-stage renal disease (18 → 15 percent), and coronary artery disease (28 → 24 percent). The average improvement in quality-adjusted life year (QALY) was 0.35 and the incremental cost-effectiveness ratio was $33,386/QALY.
Conclusions
During the first 4 years of the HDC, multiple improvements in diabetes care were observed. If these improvements are maintained or enhanced over the lifetime of patients, the HDC program will be cost-effective for society based on traditionally accepted thresholds.
doi:10.1111/j.1475-6773.2007.00734.x
PMCID: PMC2151395  PMID: 17995559
Quality improvement; cost-effectiveness analysis; safety net providers
24.  Composition and Morphology of Nanocrystals in Urines of Lithogenic Patients and Healthy Persons 
The composition and morphology of nanocrystals in urines of healthy persons and lithogenic patients were comparatively investigated by means of X-ray diffraction (XRD) and transmission electron microscopy (TEM). It was shown that the main composition of urinary nanocrystals in healthy persons were calcium oxalate dihydrate (COD), uric acid, and ammonium magnesium phosphate (struvite). However, the main compositions of urinary nanocrystals in lithogenic patients were struvite, β-tricalcium phosphate, uric acid, COD, and calcium oxalate monohydrate (COM). According to the XRD data, the size of nanocrystals was calculated to be 23∼72 nm in healthy urine and 12∼118 nm in lithogenic urine by Scherer formula. TEM results showed that the nanocrystals in healthy urine were dispersive and uniform with a mean size of about 38 nm. In contrast, the nanocrystals in lithogenic urine were much aggregated with a mean size of about 55 nm. The results in this work indicated that the urinary stone formation may be prevented by diminishing the aggregation and the size differentiation of urinary nanocrystals by physical or chemical methods.
doi:10.1155/2009/925297
PMCID: PMC2801016  PMID: 20052395
25.  Kinetic Trapping of Metastable Amino Acid Polymorphs 
Second harmonic generation (SHG) microscopy measurements indicate that inkjet-printed racemic solutions of amino acids can produce nanocrystals trapped in metastable polymorph forms upon rapid solvent evaporation. Polymorphism impacts the composition, distribution, and physicokinetic properties of organic solids, with energetic arguments favoring the most stable polymorph. In this study, unfavored noncentrosymmetric crystal forms were observed by SHG microscopy. Polarization-dependent SHG measurement and synchrotron X-ray microdiffraction analysis of individual printed drops are consistent with formation of homochiral crystal production. Fundamentally, these results provide evidence supporting the ubiquity of Ostwald’s Rule of Stages, describing the hypothesized transitioning of crystals between metastable polymorphic forms in the early stages of crystal formation. Practically, the presence of homochiral metastable forms has implications on chiral resolution and on solid form preparations relying on rapid solvent evaporation.
doi:10.1021/ja410293p
PMCID: PMC3972613  PMID: 24451055

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