scholarly journals JUNGFRAU detector for brighter x-ray sources: Solutions for IT and data science challenges in macromolecular crystallography

2020 ◽  
Vol 7 (1) ◽  
pp. 014305 ◽  
Author(s):  
Filip Leonarski ◽  
Aldo Mozzanica ◽  
Martin Brückner ◽  
Carlos Lopez-Cuenca ◽  
Sophie Redford ◽  
...  
Keyword(s):  
Data Science ◽  
Macromolecular Crystallography ◽  
X Ray

scholarly journals Electronic Excitations and Radiation Damage in Macromolecular Crystallography

Crystals ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 273 ◽  
Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi
Keyword(s):  
Chemical Information ◽  
X Rays ◽  
Electronic Excitations ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Successful Approach ◽  
Structural Research

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.

The use of dummy atoms in X-ray macromolecular crystallography

2004 ◽  
Vol 10 (4) ◽  
pp. 319-343 ◽  
Author(s):  
A. Urzhumtsev ◽  
V.Y. Lunin
Keyword(s):  
Macromolecular Crystallography ◽  
X Ray

scholarly journals Determination of X-ray flux using silicon pin diodes

2009 ◽  
Vol 16 (2) ◽  
pp. 143-151 ◽  
Author(s):  
Robin L. Owen ◽  
James M. Holton ◽  
Clemens Schulze-Briese ◽  
Elspeth F. Garman
Keyword(s):  
Light Source ◽  
Energy Deposition ◽  
Photon Flux ◽  
Macromolecular Crystallography ◽  
Pin Diodes ◽  
Web Based ◽  
X Ray ◽  
Swiss Light Source ◽  
Flux Incident

Accurate measurement of photon flux from an X-ray source, a parameter required to calculate the dose absorbed by the sample, is not yet routinely available at macromolecular crystallography beamlines. The development of a model for determining the photon flux incident on pin diodes is described here, and has been tested on the macromolecular crystallography beamlines at both the Swiss Light Source, Villigen, Switzerland, and the Advanced Light Source, Berkeley, USA, at energies between 4 and 18 keV. These experiments have shown that a simple model based on energy deposition in silicon is sufficient for determining the flux incident on high-quality silicon pin diodes. The derivation and validation of this model is presented, and a web-based tool for the use of the macromolecular crystallography and wider synchrotron community is introduced.

scholarly journals Electronic Excitations and Radiation Damage in Macromolecular Crystallography

2018 ◽  
Author(s):  
José Brandão-Neto ◽  
Leonardo Bernasconi
Keyword(s):  
Chemical Information ◽  
X Rays ◽  
Electronic Excitations ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Atomic Structures ◽  
Successful Approach ◽  
Structural Research

Macromolecular crystallography at cryogenic temperatures has so far provided the majority of the experimental evidence that underpins the determination of the atomic structures of proteins and other biomolecular assemblies by means of single crystal X-ray diffraction experiments. One of the core limitations of the current methods is that crystal samples degrade as they are subject to X-rays, and two broad groups of effects are observed: global and specific damage. While the currently successful approach is to operate outside the range where global damage is observed, specific damage is not well understood and may lead to poor interpretation of the chemistry and biology of the system under study. In this work, we present a phenomenological model in which specific damage is understood as the result of a single process, the steady excitation of crystal electrons caused by X-ray absorption, which acts as a trigger for the bulk effects that manifest themselves in the form of global damage and obscure the interpretation of chemical information from XFEL and synchrotron structural research.

scholarly journals A drug discovery-oriented non-invasive protocol for protein crystal cryoprotection by dehydration, with application for crystallization screening.

2021 ◽  
Author(s):  
Dom Bellini
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Protein Crystal ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Water Fraction ◽  
Non Invasive ◽  
Vapour Diffusion ◽  
Large Compound ◽  
Fragment Libraries

In X-ray macromolecular crystallography, cryoprotection of crystals mounted on harvesting loops is achieved when the water in the sample solvent transitions to vitreous ice before crystalline ice forms. This is achieved by rapid cooling in liquid nitrogen or propane. Protocols for protein crystal cryoprotection are based on either increasing environmental pressure or reducing the water fraction in the solvent. This study presents a new protocol for cryoprotecting crystals. It is based on vapour diffusion dehydration of the crystal drop to reduce the water fraction in the solvent by adding a highly concentrated salt solution, 13 M potassium formate (KF13), directly to the reservoir. Cryoprotection by the KF13 protocol is non-invasive to the crystal, high throughput, not labour intensive, can benefit diffraction resolution and ligand binding, and is very useful in cases with high redundancy such as drug discovery projects which utilize very large compound or fragment libraries. Moreover, an application of KF13 to discover new crystal hits from clear drops of equilibrated crystallization screening plates is also shown.

scholarly journals NSLS-II MX beamlines FMX for micro-crystallography & AMX for highly automated MX

2014 ◽  
Vol 70 (a1) ◽  
pp. C1733-C1733
Author(s):  
Martin Fuchs ◽  
Robert Sweet ◽  
Lonny Berman ◽  
Dileep Bhogadi ◽  
Wayne Hendrickson ◽  
...  
Keyword(s):  
Energy Range ◽  
Structure Determination ◽  
Optical Systems ◽  
Photon Flux ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
Binding Studies ◽  
X Ray ◽  
Array Detectors ◽  
Broad Energy Range

We present the final design of the x-ray optical systems and experimental stations of the two macromolecular crystallography (MX) beamlines, FMX and AMX, at the National Synchrotron Light Source-II (NSLS-II). Along with its companion x-ray scattering beamline, LIX, this suite of Advanced Beamlines for Biological Investigations with X-rays (ABBIX, [1]) will begin user operation in 2016. The pair of MX beamlines with complementary and overlapping capabilities is located at canted undulators (IVU21) in sector 17-ID. The Frontier Microfocusing Macromolecular Crystallography beamline (FMX) will deliver a photon flux of ~5x10^12 ph/s at a wavelength of 1 Å into a spot of 1 - 50 µm size. It will cover a broad energy range from 5 - 30 keV, corresponding to wavelengths from 0.4 - 2.5 Å. The highly Automated Macromolecular Crystallography beamline (AMX) will be optimized for high throughput applications, with beam sizes from 4 - 100 µm, an energy range of 5 - 18 keV (0.7 - 2.5 Å), and a flux at 1 Å of ~10^13 ph/s. Central components of the in-house-developed experimental stations are a 100 nm sphere of confusion goniometer with a horizontal axis, piezo-slits to provide dynamic beam size changes during diffraction experiments, a dedicated secondary goniometer for crystallization plates, and sample- and plate-changing robots. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and data collection of crystals in trays, for instance to characterize membrane protein crystals and to conduct ligand-binding studies. Together with the solution scattering program at LIX, the new beamlines will offer unique opportunities for advanced diffraction experiments with micro- and mini-beams, with next generation hybrid pixel array detectors and emerging crystal delivery methods such as acoustic droplet ejection. This work is supported by the US National Institutes of Health.

scholarly journals The Role of Validation in Macromolecular Crystallography

1998 ◽  
Vol 54 (6) ◽  
pp. 1109-1118 ◽  
Author(s):  
Eleanor Dodson
Keyword(s):  
Structure Determination ◽  
Atomic Resolution ◽  
File Format ◽  
Macromolecular Crystallography ◽  
X Ray

The importance of validation techniques in X-ray structure determination and their relation to refinement procedures are discussed, with particular reference to atomic resolution structures. The requirements of deposition and publication, and the role of validation tools in this are analysed. The need for a rigorously defined file format is emphasized.

Paleoenvironmental reconstruction of the central Levantine Corridor during the Pliocene: insights from lacustrine settings 

2021 ◽  
Author(s):  
John Greenlee ◽  
Silas Dean ◽  
Nicolas Waldmann
Keyword(s):  
High Resolution ◽  
Data Science ◽  
Environmental Changes ◽  
Laser Diffraction ◽  
Climatic Conditions ◽  
Paleoenvironmental Reconstruction ◽  
Cosmogenic Isotopes ◽  
X Ray ◽  
Geochemical Proxies ◽  
Favorable Conditions

<p>This study aims to reconstruct the paleoenvironmental and climatic conditions affecting the Levantine corridor during the early Pliocene. For the purpose of this study, a ~20 m continuous core sequence was retrieved out of the ~200 m long, tilted Erk el Ahmar sequence previously dated by cosmogenic isotopes to ~3.5 Ma. The record include intercalating units consisting of sands, silts, and clays that were sampled in high resolution in order to analyze a variety of sedimentological and geochemical proxies of past climate and environmental changes. We present new preliminary, high-resolution sedimentological (laser diffraction granulometry), petrophysical (magnetic susceptibility) and compositional (X-ray fluorescence) data along with accompanying statistical analysis performed with an advanced suite of data-science tools. These results reveal new cycles of environmental change in the area, which appears to be orbitally controlled, and include dramatic changes also indicated by discrete strata of fossil fragments. Moreover, cycles of deposition can also provide hints on the major hydrological controlling mechanisms. This project provides new light into favorable conditions for the subsistence of perennial lake environments in the Levantine Corridor, which in turn may have facilitated faunal migration between Africa and Eurasia.</p>

X-ray and neutron macromolecular crystallography

2012 ◽  
pp. 838-882
Author(s):  
Igor N. Serdyuk ◽  
Nathan R. Zaccai ◽  
Joseph Zaccai
Keyword(s):  
Macromolecular Crystallography ◽  
X Ray

scholarly journals Automated harvesting and processing of protein crystals through laser photoablation

2016 ◽  
Vol 72 (4) ◽  
pp. 454-466 ◽  
Author(s):  
Ulrich Zander ◽  
Guillaume Hoffmann ◽  
Irina Cornaciu ◽  
Jean-Pierre Marquette ◽  
Gergely Papp ◽  
...  
Keyword(s):  
Data Collection ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
New Methods ◽  
Repeated Sample ◽  
Sample Recovery ◽  
Through Diffusion ◽  
X Ray Background ◽  
Low X

Currently, macromolecular crystallography projects often require the use of highly automated facilities for crystallization and X-ray data collection. However, crystal harvesting and processing largely depend on manual operations. Here, a series of new methods are presented based on the use of a low X-ray-background film as a crystallization support and a photoablation laser that enable the automation of major operations required for the preparation of crystals for X-ray diffraction experiments. In this approach, the controlled removal of the mother liquor before crystal mounting simplifies the cryocooling process, in many cases eliminating the use of cryoprotectant agents, while crystal-soaking experiments are performed through diffusion, precluding the need for repeated sample-recovery and transfer operations. Moreover, the high-precision laser enables new mounting strategies that are not accessible through other methods. This approach bridges an important gap in automation and can contribute to expanding the capabilities of modern macromolecular crystallography facilities.

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