The use of longer X-ray wavelengths in macromolecular crystallography for sulfur SAD structure determination

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.

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The Role of Validation in Macromolecular Crystallography

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444998007136 ◽

1998 ◽

Vol 54 (6) ◽

pp. 1109-1118 ◽

Cited By ~ 2

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.

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The State of the Canadian Macromolecular Crystallography Facility

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314082643 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1735-C1735

Author(s):

James Gorin ◽

Shaunivan Labiuk ◽

Julien Cotelesage ◽

Kathryn Janzen ◽

Michel Fodje ◽

...

Keyword(s):

Data Collection ◽

Light Source ◽

Structure Determination ◽

Low Energy ◽

Air Bearing ◽

Beam Size ◽

Macromolecular Crystallography ◽

X Ray Diffraction ◽

X Ray ◽

Data Management Software

The Canadian Macromolecular Crystallography Facility (CMCF) at the Canadian Light Source consists of two macromolecular crystallography beamlines for structure determination using x-ray diffraction. The equipment at the CMCF beamlines have undergone or will undergo changes and improvements to better meet the needs of the most challenging experiments users may present. Among these improvements are: 1) Automounter improvements; 2) Better goniometry on 08ID-1 with the addition of a Huber air-bearing goniometer; 3) Added beam size capabilities on 08ID-1 with the addition of a multiple beam defining aperture holder; 4) XAFS capability on 08B1-1; 5) Improved low energy S-SAD data collection with the addition of a Helium path; 6) Improvements to the data collection and data management software; 7) A vacuum path for scattering experiments with detector distances up to 1 m; 8) A comprehensive beamline upgrade project on the 08ID-1 beamline; and 9) Service crystallography services.

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Online collection and analysis of X-ray fluorescence spectra on the macromolecular crystallography beamlines of the ESRF

Journal of Applied Crystallography ◽

10.1107/s0021889809001721 ◽

2009 ◽

Vol 42 (2) ◽

pp. 333-335 ◽

Cited By ~ 17

Author(s):

Gordon A. Leonard ◽

V. Armando Solé ◽

Antonia Beteva ◽

José Gabadinho ◽

Matias Guijarro ◽

...

Keyword(s):

Qualitative Analysis ◽

Structure Determination ◽

Fluorescence Spectra ◽

High Sensitivity ◽

Experimental Setup ◽

Biological Macromolecules ◽

Macromolecular Crystallography ◽

X Ray ◽

Additional Information

X-ray fluorescence (XRF) measurements on solutions or crystals of biological macromolecules provide additional information that can be used in structure determination and/or refinement protocols. Here details are presented of an experimental setup, employed on all the ESRF Macromolecular Crystallography Group beamlines, that allows the online collection and qualitative analysis of XRF spectra. This experimental setup uses a highly attenuated beam and short exposures, meaning it is minimally destructive but retains high sensitivity.

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Mix and Inject: Reaction Initiation by Diffusion for Time-Resolved Macromolecular Crystallography

Advances in Condensed Matter Physics ◽

10.1155/2013/167276 ◽

2013 ◽

Vol 2013 ◽

pp. 1-10 ◽

Cited By ~ 59

Author(s):

Marius Schmidt

Keyword(s):

Chemical Kinetics ◽

Structure Determination ◽

Macromolecular Crystallography ◽

Time Resolved ◽

X Ray ◽

Transient States ◽

Kinetic Mechanisms ◽

Active Substrate ◽

Reaction Initiation

Time-resolved macromolecular crystallography unifies structure determination with chemical kinetics, since the structures of transient states and chemical and kinetic mechanisms can be determined simultaneously from the same data. To start a reaction in an enzyme, typically, an initially inactive substrate present in the crystal is activated. This has particular disadvantages that are circumvented when active substrate is directly provided by diffusion. However, then it is prohibitive to use macroscopic crystals because diffusion times become too long. With small micro- and nanocrystals diffusion times are adequately short for most enzymes and the reaction can be swiftly initiated. We demonstrate here that a time-resolved crystallographic experiment becomes feasible by mixing substrate with enzyme nanocrystals which are subsequently injected into the X-ray beam of a pulsed X-ray source.

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A study on α-RuCl3 crystal structure by scanning tunneling microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100152124 ◽

1989 ◽

Vol 47 ◽

pp. 30-31

Author(s):

H.-J. Cantow ◽

H. Hillebrecht ◽

S. Magonov ◽

H. W. Rotter ◽

G. Thiele

Keyword(s):

Crystal Structure ◽

Density Distribution ◽

Scanning Tunneling Microscopy ◽

Electron Density ◽

Structure Determination ◽

Electron Density Distribution ◽

Scanning Tunneling ◽

Monoclinic Space Group ◽

Tunneling Microscopy ◽

X Ray

From X-ray analysis, the conclusions are drawn from averaged molecular informations. Thus, limitations are caused when analyzing systems whose symmetry is reduced due to interatomic interactions. In contrast, scanning tunneling microscopy (STM) directly images atomic scale surface electron density distribution, with a resolution up to fractions of Angstrom units. The crucial point is the correlation between the electron density distribution and the localization of individual atoms, which is reasonable in many cases. Thus, the use of STM images for crystal structure determination may be permitted. We tried to apply RuCl3 - a layered material with semiconductive properties - for such STM studies. From the X-ray analysis it has been assumed that α-form of this compound crystallizes in the monoclinic space group C2/m (AICI3 type). The chlorine atoms form an almost undistorted cubic closed package while Ru occupies 2/3 of the octahedral holes in every second layer building up a plane hexagon net (graphite net). Idealizing the arrangement of the chlorines a hexagonal symmetry would be expected. X-ray structure determination of isotypic compounds e.g. IrBr3 leads only to averaged positions of the metal atoms as there exist extended stacking faults of the metal layers.

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