graph Heliograph: optische Telegraphie: eine leichtverständliche Anleitung zur Selbstherstellung eines Apparates zum Telegraphieren mit Hilfe des Lichtes / von Arthur Gruber ; mit zwei Modellbogen By library.mit.edu Published On :: Sun, 28 Sep 2014 08:10:12 EDT Archives, Room Use Only - UG582.H4 G78 1920z Full Article
graph The Western Union Telegraph Company: rules. By library.mit.edu Published On :: Sun, 28 Sep 2014 08:10:12 EDT Archives, Room Use Only - HE7797.W53 W47 1884 Full Article
graph General railroad and telegraph laws of the State of Pennsylvania: including the acts relating to incline plane railways and street passenger railways, and such acts relative to corporations as affect railroad and telegraph companies, 1816-1883 / comp. and By library.mit.edu Published On :: Sun, 28 Sep 2014 08:10:12 EDT Archives, Room Use Only - KFP301.A3 1884 Full Article
graph On submerging telegraphic cables / by James Atkinson Longridge , M. Inst. C.E., and Charles Henry Brooks By library.mit.edu Published On :: Sun, 28 Sep 2014 08:10:12 EDT Archives, Room Use Only - TK5671.L66 1858 Full Article
graph [Collection of Atlantic, Lake and Mississippi Telegraph items]. By library.mit.edu Published On :: Sun, 13 Sep 2015 06:37:39 EDT Archives, Room Use Only - TK5123.6.C65 1847 Full Article
graph [Collection of Atlantic, Lake and Mississippi Telegraph pamphlets]. By library.mit.edu Published On :: Sun, 13 Sep 2015 06:37:39 EDT Archives, Room Use Only - TK5123.6.C66 1847 Full Article
graph [Collection of Atlantic, Lake and Mississippi Telegraph circulars]. By library.mit.edu Published On :: Sun, 13 Sep 2015 06:37:39 EDT Archives, Room Use Only - TK5123.6.C665 1847 Full Article
graph Handbook of aerial construction / the Central District and Printing Telegraph Company By library.mit.edu Published On :: Sun, 2 Apr 2017 06:39:00 EDT Archives, Room Use Only - TK5455.H36 1908 Full Article
graph Die Funkentelegraphie / von H. Thurn By library.mit.edu Published On :: Sun, 8 Oct 2017 06:45:21 EDT Archives, Room Use Only - TK5742.T48 1913 Full Article
graph Mumbai photographer thrashed by cops at CAA protest By www.rediff.com Published On :: Fri, 07 Feb 2020 09:30:07 +0530 Ashish Raje, a photojournalist with a Mumbai tabloid, was allegedly pushed and assaulted by two police officials when he was walking to Mumbai Bagh in Nagpada area. Full Article Anil Deshmukh Mumbai Press Club CAA Ashish Raje Mumbai Police Maharashtra Delhi Nagpada
graph These underwater photographs are just unforgettable! By www.rediff.com Published On :: Wed, 04 Mar 2020 09:48:25 +0530 Underwater Photographer of the Year celebrates photography beneath the surface of the ocean, lakes and rivers.More than 5,500 underwater pictures were entered in 13 categories by underwater photographers from 70 countries around the world.Scroll down to see the winning images. Full Article UPY2020 Jessica Hannah Yucatan Peninsula of Mexico RIB Mok Wai Hoe Frozen Mobile Home Scott Gutsy Tuason west coast of Scotland Greg Lecoeur Colin Garrett Arthur Kingdon Zena Holloway James Lynott Anita Kainrath Rooman Luc Flavia Eberhard
graph Extraordinary winners of Sony World Photography Awards By www.rediff.com Published On :: Thu, 12 Mar 2020 08:37:12 +0530 From incredible landscapes to touching portraits to memorable wildlife photography, the winners of the Sony World Photography Awards showcase it all!Scroll down and prepared to be wowed... Full Article Sony World Kazakh Bitlis Via Ferrata De Luca-Innerkofler Young Eagle Hunter Lady Golden Eagle Festival Onguma Private Reserve Kyaw Bo Bo Mongolia Pobitora Wildlife Sanctuary Bermamyt Plateau Tien Sang Karem Apaza Monkey Forest Abhijeet Kumar Assam India
graph Breathtaking images from Sony World Photography Awards By www.rediff.com Published On :: Mon, 20 Apr 2020 08:18:20 +0530 Behold the breathtaking winning and shortlisted images from one of the world's most prestigious photography contests.The amazing shots are from the open competition of the Sony World Photography Awards 2020, which received 193,000 entries from photographers in over 200 territories.Scroll down and feast your eyes on our pick of the shortlisted and category-winning entries. Full Article World Photography Awards Peter Brooks David Keep Black Francis Hsiang Hui Muriel Vekemans Jorge Reynal Santiaga Mesa Lloyd Lane Craig McGowan Alec Connah Ironbridge Power Station in Shropshire James Rushforth Guofei Li Sylvester Wong Julia Wimmerlin
graph Prince Harry-Meghan Markle's biography 'Finding Freedom' to... By Published On :: Prince Harry-Meghan Markle's biography 'Finding Freedom' to... Full Article
graph Maradona autographs shirt to help poor By Published On :: Maradona autographs shirt to help poor Full Article
graph Fast identification of mineral inclusions in diamond at GSECARS using synchrotron X-ray microtomography, radiography and diffraction By scripts.iucr.org Published On :: 2019-07-19 Mineral inclusions in natural diamond are widely studied for the insight that they provide into the geochemistry and dynamics of the Earth's interior. A major challenge in achieving thorough yet high rates of analysis of mineral inclusions in diamond derives from the micrometre-scale of most inclusions, often requiring synchrotron radiation sources for diffraction. Centering microinclusions for diffraction with a highly focused synchrotron beam cannot be achieved optically because of the very high index of refraction of diamond. A fast, high-throughput method for identification of micromineral inclusions in diamond has been developed at the GeoSoilEnviro Center for Advanced Radiation Sources (GSECARS), Advanced Photon Source, Argonne National Laboratory, USA. Diamonds and their inclusions are imaged using synchrotron 3D computed X-ray microtomography on beamline 13-BM-D of GSECARS. The location of every inclusion is then pinpointed onto the coordinate system of the six-circle goniometer of the single-crystal diffractometer on beamline 13-BM-C. Because the bending magnet branch 13-BM is divided and delivered into 13-BM-C and 13-BM-D stations simultaneously, numerous diamonds can be examined during coordinated runs. The fast, high-throughput capability of the methodology is demonstrated by collecting 3D diffraction data on 53 diamond inclusions from Juína, Brazil, within a total of about 72 h of beam time. Full Article text
graph Soft X-ray varied-line-spacing gratings fabricated by near-field holography using an electron beam lithography-written phase mask By scripts.iucr.org Published On :: 2019-08-16 A fabrication method comprising near-field holography (NFH) with an electron beam lithography (EBL)-written phase mask was developed to fabricate soft X-ray varied-line-spacing gratings (VLSGs). An EBL-written phase mask with an area of 52 mm × 30 mm and a central line density greater than 3000 lines mm−1 was used. The introduction of the EBL-written phase mask substantially simplified the NFH optics for pattern transfer. The characterization of the groove density distribution and diffraction efficiency of the fabricated VLSGs indicates that the EBL–NFH method is feasible and promising for achieving high-accuracy groove density distributions with corresponding image properties. Vertical stray light is suppressed in the soft X-ray spectral range. Full Article text
graph Reducing sample consumption for serial crystallography using acoustic drop ejection By scripts.iucr.org Published On :: 2019-08-16 Efficient sample delivery is an essential aspect of serial crystallography at both synchrotrons and X-ray free-electron lasers. Rastering fixed target chips through the X-ray beam is an efficient method for serial delivery from the perspectives of both sample consumption and beam time usage. Here, an approach for loading fixed targets using acoustic drop ejection is presented that does not compromise crystal quality, can reduce sample consumption by more than an order of magnitude and allows serial diffraction to be collected from a larger proportion of the crystals in the slurry. Full Article text
graph X-ray fluorescence detection for serial macromolecular crystallography using a JUNGFRAU pixel detector By scripts.iucr.org Published On :: 2020-02-07 Detection of heavy elements, such as metals, in macromolecular crystallography (MX) samples by X-ray fluorescence is a function traditionally covered at synchrotron MX beamlines by silicon drift detectors, which cannot be used at X-ray free-electron lasers because of the very short duration of the X-ray pulses. Here it is shown that the hybrid pixel charge-integrating detector JUNGFRAU can fulfill this function when operating in a low-flux regime. The feasibility of precise position determination of micrometre-sized metal marks is also demonstrated, to be used as fiducials for offline prelocation in serial crystallography experiments, based on the specific fluorescence signal measured with JUNGFRAU, both at the synchrotron and at SwissFEL. Finally, the measurement of elemental absorption edges at a synchrotron beamline using JUNGFRAU is also demonstrated. Full Article text
graph Limited angle tomography for transmission X-ray microscopy using deep learning By scripts.iucr.org Published On :: 2020-02-13 In transmission X-ray microscopy (TXM) systems, the rotation of a scanned sample might be restricted to a limited angular range to avoid collision with other system parts or high attenuation at certain tilting angles. Image reconstruction from such limited angle data suffers from artifacts because of missing data. In this work, deep learning is applied to limited angle reconstruction in TXMs for the first time. With the challenge to obtain sufficient real data for training, training a deep neural network from synthetic data is investigated. In particular, U-Net, the state-of-the-art neural network in biomedical imaging, is trained from synthetic ellipsoid data and multi-category data to reduce artifacts in filtered back-projection (FBP) reconstruction images. The proposed method is evaluated on synthetic data and real scanned chlorella data in 100° limited angle tomography. For synthetic test data, U-Net significantly reduces the root-mean-square error (RMSE) from 2.55 × 10−3 µm−1 in the FBP reconstruction to 1.21 × 10−3 µm−1 in the U-Net reconstruction and also improves the structural similarity (SSIM) index from 0.625 to 0.920. With penalized weighted least-square denoising of measured projections, the RMSE and SSIM are further improved to 1.16 × 10−3 µm−1 and 0.932, respectively. For real test data, the proposed method remarkably improves the 3D visualization of the subcellular structures in the chlorella cell, which indicates its important value for nanoscale imaging in biology, nanoscience and materials science. Full Article text
graph The HARE chip for efficient time-resolved serial synchrotron crystallography By scripts.iucr.org Published On :: 2020-02-27 Serial synchrotron crystallography (SSX) is an emerging technique for static and time-resolved protein structure determination. Using specifically patterned silicon chips for sample delivery, the `hit-and-return' (HARE) protocol allows for efficient time-resolved data collection. The specific pattern of the crystal wells in the HARE chip provides direct access to many discrete time points. HARE chips allow for optical excitation as well as on-chip mixing for reaction initiation, making a large number of protein systems amenable to time-resolved studies. Loading of protein microcrystals onto the HARE chip is streamlined by a novel vacuum loading platform that allows fine-tuning of suction strength while maintaining a humid environment to prevent crystal dehydration. To enable the widespread use of time-resolved serial synchrotron crystallography (TR-SSX), detailed technical descriptions of a set of accessories that facilitate TR-SSX workflows are provided. Full Article text
graph Tomographic reconstruction with a generative adversarial network By scripts.iucr.org Published On :: 2020-02-18 This paper presents a deep learning algorithm for tomographic reconstruction (GANrec). The algorithm uses a generative adversarial network (GAN) to solve the inverse of the Radon transform directly. It works for independent sinograms without additional training steps. The GAN has been developed to fit the input sinogram with the model sinogram generated from the predicted reconstruction. Good quality reconstructions can be obtained during the minimization of the fitting errors. The reconstruction is a self-training procedure based on the physics model, instead of on training data. The algorithm showed significant improvements in the reconstruction accuracy, especially for missing-wedge tomography acquired at less than 180° rotational range. It was also validated by reconstructing a missing-wedge X-ray ptychographic tomography (PXCT) data set of a macroporous zeolite particle, for which only 51 projections over 70° could be collected. The GANrec recovered the 3D pore structure with reasonable quality for further analysis. This reconstruction concept can work universally for most of the ill-posed inverse problems if the forward model is well defined, such as phase retrieval of in-line phase-contrast imaging. Full Article text
graph The indexing ambiguity in serial femtosecond crystallography (SFX) resolved using an expectation maximization algorithm By journals.iucr.org Published On :: An expectation maximization algorithm is implemented to resolve the indexing ambiguity which arises when merging data from many crystals in protein crystallography, especially in cases where partial reflections are recorded in serial femtosecond crystallography (SFX) at XFELs. Full Article text
graph Nanocrystalline materials: recent advances in crystallographic characterization techniques By journals.iucr.org Published On :: This feature article reviews the control and understanding of nanoparticle shape from their crystallography and growth. Particular emphasis is placed on systems relevant for plasmonics and catalysis. Full Article text
graph Binding site asymmetry in human transthyretin: insights from a joint neutron and X-ray crystallographic analysis using perdeuterated protein By journals.iucr.org Published On :: A neutron crystallographic study of perdeuterated transthyretin reveals important aspects of the structure relating to its stability and its propensity to form fibrils, as well as evidence of a single water molecule that affects the symmetry of the two binding pockets. Full Article text
graph Chemical crystallography and crystal engineering By journals.iucr.org Published On :: Today, there is very little doubt that chemistry owes as much to crystallography as crystallography does to chemistry. This mutual synergy defines modern chemical crystallography. Full Article text
graph True North to align with Magnetic North at Greenwich for first time in 360 years - Telegraph.co.uk By www.telegraph.co.uk Published On :: Fri, 30 Aug 2019 07:00:00 GMT True North to align with Magnetic North at Greenwich for first time in 360 years Telegraph.co.uk Full Article
graph Oil workers in North Sea feel effects of earthquake, with platform 'shaking' - Evening Telegraph By www.eveningtelegraph.co.uk Published On :: Wed, 25 Sep 2019 07:00:00 GMT Oil workers in North Sea feel effects of earthquake, with platform 'shaking' Evening Telegraph Full Article
graph Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport By scripts.iucr.org Published On :: 2020-04-29 The transmembrane intracellular lectin ER–Golgi intermediate compartment protein 53 (ERGIC-53) and the soluble EF-hand multiple coagulation factor deficiency protein 2 (MCFD2) form a complex that functions as a cargo receptor, trafficking various glycoproteins between the endoplasmic reticulum (ER) and the Golgi apparatus. It has been demonstrated that the carbohydrate-recognition domain (CRD) of ERGIC-53 (ERGIC-53CRD) interacts with N-linked glycans on cargo glycoproteins, whereas MCFD2 recognizes polypeptide segments of cargo glycoproteins. Crystal structures of ERGIC-53CRD complexed with MCFD2 and mannosyl oligosaccharides have revealed protein–protein and protein–sugar binding modes. In contrast, the polypeptide-recognition mechanism of MCFD2 remains largely unknown. Here, a 1.60 Å resolution crystal structure of the ERGIC-53CRD–MCFD2 complex is reported, along with three other crystal forms. Comparison of these structures with those previously reported reveal that MCFD2, but not ERGIC-53–CRD, exhibits significant conformational plasticity that may be relevant to its accommodation of various polypeptide ligands. Full Article text
graph Macromolecular X-ray crystallography: soon to be a road less travelled? By journals.iucr.org Published On :: From the perspective of a young(ish) structural biologist who currently specialises in macromolecular X-ray crystallography, are the best years of crystallography over? Some evidence and hopefully thought-provoking analysis is presented here on the subject. Full Article text
graph 3D-printed holders for in meso in situ fixed-target serial X-ray crystallography By scripts.iucr.org Published On :: 2020-04-23 The in meso in situ serial X-ray crystallography method was developed to ease the handling of small fragile crystals of membrane proteins and for rapid data collection on hundreds of microcrystals directly in the growth medium without the need for crystal harvesting. To facilitate mounting of these in situ samples on a goniometer at cryogenic or at room temperatures, two new 3D-printed holders have been developed. They provide for cubic and sponge phase sample stability in the X-ray beam and are compatible with sample-changing robots. The holders can accommodate a variety of window material types, as well as bespoke samples for diffraction screening and data collection at conventional macromolecular crystallography beamlines. They can be used for convenient post-crystallization treatments such as ligand and heavy-atom soaking. The design, assembly and application of the holders for in situ serial crystallography are described. Files for making the holders using a 3D printer are included as supporting information. Full Article text
graph Journal of Applied Crystallography By journals.iucr.org Published On :: Full Article Still image
graph Radiation damage in small-molecule crystallography: fact not fiction By scripts.iucr.org Published On :: 2019-06-14 Traditionally small-molecule crystallographers have not usually observed or recognized significant radiation damage to their samples during diffraction experiments. However, the increased flux densities provided by third-generation synchrotrons have resulted in increasing numbers of observations of this phenomenon. The diversity of types of small-molecule systems means it is not yet possible to propose a general mechanism for their radiation-induced sample decay, however characterization of the effects will permit attempts to understand and mitigate it. Here, systematic experiments are reported on the effects that sample temperature and beam attenuation have on radiation damage progression, allowing qualitative and quantitative assessment of their impact on crystals of a small-molecule test sample. To allow inter-comparison of different measurements, radiation-damage metrics (diffraction-intensity decline, resolution fall-off, scaling B-factor increase) are plotted against the absorbed dose. For ease-of-dose calculations, the software developed for protein crystallography, RADDOSE-3D, has been modified for use in small-molecule crystallography. It is intended that these initial experiments will assist in establishing protocols for small-molecule crystallographers to optimize the diffraction signal from their samples prior to the onset of the deleterious effects of radiation damage. Full Article text
graph On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies By scripts.iucr.org Published On :: 2019-06-19 Efficient and reliable sample delivery has remained one of the bottlenecks for serial crystallography experiments. Compared with other methods, fixed-target sample delivery offers the advantage of significantly reduced sample consumption and shorter data collection times owing to higher hit rates. Here, a new method of on-chip crystallization is reported which allows the efficient and reproducible growth of large numbers of protein crystals directly on micro-patterned silicon chips for in-situ serial crystallography experiments. Crystals are grown by sitting-drop vapor diffusion and previously established crystallization conditions can be directly applied. By reducing the number of crystal-handling steps, the method is particularly well suited for sensitive crystal systems. Excessive mother liquor can be efficiently removed from the crystals by blotting, and no sealing of the fixed-target sample holders is required to prevent the crystals from dehydrating. As a consequence, `naked' crystals are obtained on the chip, resulting in very low background scattering levels and making the crystals highly accessible for external manipulation such as the application of ligand solutions. Serial diffraction experiments carried out at cryogenic temperatures at a synchrotron and at room temperature at an X-ray free-electron laser yielded high-quality X-ray structures of the human membrane protein aquaporin 2 and two new ligand-bound structures of thermolysin and the human kinase DRAK2. The results highlight the applicability of the method for future high-throughput on-chip screening of pharmaceutical compounds. Full Article text
graph Screening topological materials with a CsCl-type structure in crystallographic databases By scripts.iucr.org Published On :: 2019-06-13 CsCl-type materials have many outstanding characteristics, i.e. simple in structure, ease of synthesis and good stability at room temperature, thus are an excellent choice for designing functional materials. Using high-throughput first-principles calculations, a large number of topological semimetals/metals (TMs) were designed from CsCl-type materials found in crystallographic databases and their crystal and electronic structures have been studied. The CsCl-type TMs in this work show rich topological character, ranging from triple nodal points, type-I nodal lines and critical-type nodal lines, to hybrid nodal lines. The TMs identified show clean topological band structures near the Fermi level, which are suitable for experimental investigations and future applications. This work provides a rich data set of TMs with a CsCl-type structure. Full Article text
graph Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps By scripts.iucr.org Published On :: 2019-06-27 Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator, an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool. Full Article text
graph Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography By scripts.iucr.org Published On :: 2019-06-23 Copper-containing nitrite reductases (CuNiRs) that convert NO2− to NO via a CuCAT–His–Cys–CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD−, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2− a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed. Full Article text
graph 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector By scripts.iucr.org Published On :: 2019-08-17 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. Full Article text
graph Crystallographic insights into diamond-shaped 7M martensite in Ni–Mn–Ga ferromagnetic shape-memory alloys By scripts.iucr.org Published On :: 2019-08-15 For Heusler-type Ni–Mn–Ga ferromagnetic shape-memory alloys, the configuration of the martensite variants is a decisive factor in achieving a large magnetic shape-memory effect through field-induced variant reorientation. Based upon the spatially resolved electron backscatter diffraction technique, the microstructural evolution associated with the martensitic transformation from austenite to seven-layered modulated (7M) martensite was investigated on a polycrystalline Ni53Mn22Ga25 alloy. It was clearly shown that grain interior nucleation led to the formation of diamond-shaped 7M martensite within the parent austenite matrix. This diamond microstructure underwent further growth through an isotropic expansion with the coordinated outward movement of four side habit planes, followed by an anisotropic elongation with the forward extension of a type-I twin pair. A two-step growth model is proposed to describe the specific morphology and crystallography of 7M martensite. In addition, the habit planes were revealed to possess a stepped structure, with the {1 0 1}A plane as the terrace and the {0 1 0}A plane as the step. The characteristic combination of martensite variants and the underlying mechanism of self-accommodation in the martensitic transformation have been analysed in terms of the minimum total transformation strain, where the deformation gradient matrix was constructed according to the experimentally determined orientation relationship between the two phases. The present results may deepen the understanding of special martensite microstructures during the martensitic transformation in ferromagnetic shape-memory alloys. Full Article text
graph Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult? By scripts.iucr.org Published On :: 2019-08-13 The interoperability of chemical and biological crystallographic data is a key challenge to research and its application to pharmaceutical design. Research attempting to combine data from the two disciplines, small-molecule or chemical crystallography (CX) and macromolecular crystallography (MX), will face unique challenges including variations in terminology, software development, file format and databases which differ significantly from CX to MX. This perspective overview spans the two disciplines and originated from the investigation of protein binding to model radiopharmaceuticals. The opportunities of interlinked research while utilizing the two databases of the CSD (Cambridge Structural Database) and the PDB (Protein Data Bank) will be highlighted. The advantages of software that can handle multiple file formats and the circuitous route to convert organometallic small-molecule structural data for use in protein refinement software will be discussed. In addition some pointers to avoid being shipwrecked will be shared, such as the care which must be taken when interpreting data precision involving small molecules versus proteins. Full Article text
graph High-throughput structures of protein–ligand complexes at room temperature using serial femtosecond crystallography By scripts.iucr.org Published On :: 2019-10-10 High-throughput X-ray crystal structures of protein–ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein–ligand complexes using SFX. Full Article text
graph A fixed-target platform for serial femtosecond crystallography in a hydrated environment By scripts.iucr.org Published On :: 2020-01-01 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. Full Article text
graph fragHAR: towards ab initio quantum-crystallographic X-ray structure refinement for polypeptides and proteins By scripts.iucr.org Published On :: 2020-01-17 The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speed-ups are observed for the larger systems. Using this approach, it is possible to perform a highly parallelized HAR in reasonable times for large systems. The method has been implemented in the TONTO software. Full Article text
graph 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow By scripts.iucr.org Published On :: 2020-01-16 Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of atomically resolved and time-resolved molecular movies. However, the study of many biologically relevant targets is still severely hindered by high sample consumption and lengthy data-collection times. By combining serial synchrotron crystallography (SSX) with 3D printing, a new experimental platform has been created that tackles these challenges. An affordable 3D-printed, X-ray-compatible microfluidic device (3D-MiXD) is reported that allows data to be collected from protein microcrystals in a 3D flow with very high hit and indexing rates, while keeping the sample consumption low. The miniaturized 3D-MiXD can be rapidly installed into virtually any synchrotron beamline with only minimal adjustments. This efficient collection scheme in combination with its mixing geometry paves the way for recording molecular movies at synchrotrons by mixing-triggered millisecond time-resolved SSX. Full Article text
graph The early history of cryo-cooling for macromolecular crystallography By scripts.iucr.org Published On :: 2020-01-25 This paper recounts the first successful cryo-cooling of protein crystals that demonstrated the reduction in X-ray damage to macromolecular crystals. The project was suggested by David C. Phillips in 1965 at the Royal Institution of Great Britain and continued in 1967 at the Weizmann Institute of Science, where the first cryo-cooling experiments were performed on lysozyme crystals, and was completed in 1969 at Purdue University on lactate dehydrogenase crystals. A 1970 publication in Acta Crystallographica described the cryo-procedures, the use of cryo-protectants to prevent ice formation, the importance of fast, isotropic cryo-cooling and the collection of analytical data showing more than a tenfold decrease in radiation damage in cryo-cooled lactate dehydrogenase crystals. This was the first demonstration of any method that reduced radiation damage in protein crystals, which provided crystallographers with suitable means to employ synchrotron X-ray sources for protein-crystal analysis. Today, fifty years later, more than 90% of the crystal structures deposited in the Protein Data Bank have been cryo-cooled. Full Article text
graph Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals By scripts.iucr.org Published On :: 2020-02-26 Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme. Full Article text
graph Scanning electron microscopy as a method for sample visualization in protein X-ray crystallography By scripts.iucr.org Published On :: 2020-04-10 Developing methods to determine high-resolution structures from micrometre- or even submicrometre-sized protein crystals has become increasingly important in recent years. This applies to both large protein complexes and membrane proteins, where protein production and the subsequent growth of large homogeneous crystals is often challenging, and to samples which yield only micro- or nanocrystals such as amyloid or viral polyhedrin proteins. The versatile macromolecular crystallography microfocus (VMXm) beamline at Diamond Light Source specializes in X-ray diffraction measurements from micro- and nanocrystals. Because of the possibility of measuring data from crystalline samples that approach the resolution limit of visible-light microscopy, the beamline design includes a scanning electron microscope (SEM) to visualize, locate and accurately centre crystals for X-ray diffraction experiments. To ensure that scanning electron microscopy is an appropriate method for sample visualization, tests were carried out to assess the effect of SEM radiation on diffraction quality. Cytoplasmic polyhedrosis virus polyhedrin protein crystals cryocooled on electron-microscopy grids were exposed to SEM radiation before X-ray diffraction data were collected. After processing the data with DIALS, no statistically significant difference in data quality was found between datasets collected from crystals exposed and not exposed to SEM radiation. This study supports the use of an SEM as a tool for the visualization of protein crystals and as an integrated visualization tool on the VMXm beamline. Full Article text
graph Well-based crystallization of lipidic cubic phase microcrystals for serial X-ray crystallography experiments By scripts.iucr.org Published On :: 2019-10-01 Serial crystallography is having an increasing impact on structural biology. This emerging technique opens up new possibilities for studying protein structures at room temperature and investigating structural dynamics using time-resolved X-ray diffraction. A limitation of the method is the intrinsic need for large quantities of well ordered micrometre-sized crystals. Here, a method is presented to screen for conditions that produce microcrystals of membrane proteins in the lipidic cubic phase using a well-based crystallization approach. A key advantage over earlier approaches is that the progress of crystal formation can be easily monitored without interrupting the crystallization process. In addition, the protocol can be scaled up to efficiently produce large quantities of crystals for serial crystallography experiments. Using the well-based crystallization methodology, novel conditions for the growth of showers of microcrystals of three different membrane proteins have been developed. Diffraction data are also presented from the first user serial crystallography experiment performed at MAX IV Laboratory. Full Article text
graph Deriving and refining atomic models in crystallography and cryo-EM: the latest Phenix tools to facilitate structure analysis By scripts.iucr.org Published On :: 2019-10-01 Full Article text