scholarly journals Future developments for macromolecular crystallography at the CLS

2014 ◽  
Vol 70 (a1) ◽  
pp. C1737-C1737
Author(s):  
Pawel Grochulski ◽  
Miroslaw Cygler ◽  
Michel Fodje ◽  
Shaunivan Labiuk ◽  
James Gorin ◽  
...  
Keyword(s):  
High Efficiency ◽  
Single Photon ◽  
Temporal Stability ◽  
Small Samples ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
Optical Elements ◽  
X Ray ◽  
Small Crystals ◽  
Reported Data

The Canadian Macromolecular Crystallography Facility (CMCF) at the Canadian Light Source (CLS) is a suite of fully automated beamlines, 08ID-1 and 08B1-1 [1]. It serves over 60 Canadian groups plus academic and commercial users in the US. Besides remote data collection, we offer Mail-In service where data are collected by CMCF staff. Beamline 08B1-1 has been in operation since 2011 and beamline 08ID-1 since 2006. When beamline 08ID-1 was designed, over 10 years ago, small crystals were defined as having sizes of 50-100 μm. Today, the most challenging experiments require more intense X-ray beams that can be focused to accommodate much smaller crystal sizes of less than 5 μm with flux on the order of 10^11 photons/s. To reach these stringent parameters, a new more powerful source of X-rays will be required, which will be provided by a longer small-gap in-vacuum undulator (SGU). To accommodate the higher power levels and to focus X-rays to a smaller focal spot with a high degree of spatial and temporal stability, the existing X-ray optical elements need to be upgraded. The remaining components of the project include a 5-axis alignment table for improving alignment of small samples with the microbeam, a high-efficiency robotic sample-changer and a single-photon X-ray detector. Several options for the new design will be discussed. These developments are consistent with the current direction of structural biology research at the CLS [2]. Since 2006 over 225 (240) papers and 400 (444) PDB deposits reported data collected at beamline 08ID-1. Parentheses indicate the total number for the CMCF. Many of these have been published in very high impact journals such as N. Engl. J. Med., Nature, Cell, Science, PNAS, among others (http://cmcf.lightsource.ca/publications/).

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.

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 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 X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules

2019 ◽  
Vol 88 (1) ◽  
pp. 35-58 ◽  
Author(s):  
Henry N. Chapman
Keyword(s):  
Free Electron ◽  
Conformational Dynamics ◽  
Cryogenic Cooling ◽  
X Rays ◽  
Free Electron Lasers ◽  
X Ray ◽  
Virus Particles ◽  
Structure And Dynamics ◽  
Small Crystals ◽  
Serial Crystallography

X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.

scholarly journals Time-Resolved Macromolecular Crystallography at Pulsed X-ray Sources

2019 ◽  
Vol 20 (6) ◽  
pp. 1401 ◽  
Author(s):  
Marius Schmidt
Keyword(s):  
Structural Biology ◽  
Free Electron ◽  
Reaction Dynamics ◽  
X Rays ◽  
Free Electron Lasers ◽  
Macromolecular Crystallography ◽  
Time Resolved ◽  
X Ray ◽  
Methodological Aspects

The focus of structural biology is shifting from the determination of static structures to the investigation of dynamical aspects of macromolecular function. With time-resolved macromolecular crystallography (TRX), intermediates that form and decay during the macromolecular reaction can be investigated, as well as their reaction dynamics. Time-resolved crystallographic methods were initially developed at synchrotrons. However, about a decade ago, extremely brilliant, femtosecond-pulsed X-ray sources, the free electron lasers for hard X-rays, became available to a wider community. TRX is now possible with femtosecond temporal resolution. This review provides an overview of methodological aspects of TRX, and at the same time, aims to outline the frontiers of this method at modern pulsed X-ray sources.

scholarly journals SPINE-compatible `carboloops': a new microshaped vitreous carbon sample mount for X-ray and neutron crystallography

2014 ◽  
Vol 70 (5) ◽  
pp. 681-684 ◽  
Author(s):  
Filippo Romoli ◽  
Estelle Mossou ◽  
Maxime Cuypers ◽  
Peter van der Linden ◽  
Philippe Carpentier ◽  
...  
Keyword(s):  
Large Scale ◽  
Production Quality ◽  
Vitreous Carbon ◽  
Scale Production ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Large Scale Production ◽  
Custom Design ◽  
High Standards

A novel vitreous carbon mount for macromolecular crystallography, suitable for neutron and X-ray crystallographic studies, has been developed. The technology described here is compatible both with X-ray and neutron cryo-crystallography. The mounts have low density and low background scattering for both neutrons and X-rays. They are prepared by laser cutting, allowing high standards of production quality, the ability to custom-design the mount to specific crystal sizes and large-scale production.

scholarly journals High-efficiency zone-plate optics for multi-keV X-ray focusing

2014 ◽  
Vol 21 (3) ◽  
pp. 497-501 ◽  
Author(s):  
Istvan Mohacsi ◽  
Petri Karvinen ◽  
Ismo Vartiainen ◽  
Vitaliy A. Guzenko ◽  
Andrea Somogyi ◽  
...  
Keyword(s):  
Optical Transmission ◽  
High Efficiency ◽  
Fresnel Zone ◽  
Transmission Function ◽  
Zone Plate ◽  
X Rays ◽  
Fresnel Zone Plates ◽  
X Ray ◽  
Zone Plates ◽  
The Ideal

High-efficiency nanofocusing of hard X-rays using stacked multilevel Fresnel zone plates with a smallest zone width of 200 nm is demonstrated. The approach is to approximate the ideal parabolic lens profile with two-, three-, four- and six-level zone plates. By stacking binary and three-level zone plates with an additional binary zone plate, the number of levels in the optical transmission function was doubled, resulting in four- and six-level profiles, respectively. Efficiencies up to 53.7% focusing were experimentally obtained with 6.5 keV photons using a compact alignment apparatus based on piezoelectric actuators. The measurements have also been compared with numerical simulations to study the misalignment of the two zone plates.

scholarly journals On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths

2007 ◽  
Vol 63 (3) ◽  
pp. 366-380 ◽  
Author(s):  
Christoph Mueller-Dieckmann ◽  
Santosh Panjikar ◽  
Andrea Schmidt ◽  
Simone Mueller ◽  
Jochen Kuper ◽  
...  
Keyword(s):  
X Rays ◽  
Macromolecular Crystallography ◽  
X Ray

scholarly journals Macromolecular crystallography using neutrons

2014 ◽  
Vol 36 (3) ◽  
pp. 40-42
Author(s):  
Matthew Blakeley
Keyword(s):  
Nucleic Acids ◽  
Biological Systems ◽  
Biological Macromolecules ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Vast Array ◽  
X Ray ◽  
Macromolecular Assemblies

When you think about macromolecular crystallography, the technique that most often comes to mind is X-ray diffraction and it's no wonder. Over 88000 structures of biological macromolecules – from proteins and nucleic acids to viruses and macromolecular assemblies – have been determined using X-rays, and these have contributed significantly to our understanding of a vast array of biological systems and processes.

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