XRD1

Welcome to XRD1 @ Elettra.

X-rays are an invaluable probe of the structure of matter, and the range of problems where X-rays have proved to be decisive in unravelling a material structure is very wide. The X-Ray Diffraction 1 (XRD1) beamline has been designed (in collaboration with the Istituto di Cristallografia - CNR) primarily for macromolecular crystallography, but the characteristics of the beamline permit to perform a wide variety of experiments. The light source is a multipole wiggler with a useful range from 4 to 21 keV. The optics consist in a vertical collimating mirror, a double-crystal Si(111) monochromator followed by a bendable focussing mirror. The multipole wiggler spectrum includes high photon flux at low energies, allowing the optimization of the anomalous signal of several heavy atoms (up to the calcium edge), and offering the enhancement of the Sulphur anomalous signal. The experimental setup consists in a Huber goniometer with k geometry fully controllable from remote. The beamline hosts small molecules, protein crystallography, powder diffraction, high pressure physics and solid-state experiments.

Research Highlights

Chemistry at the protein–mineral interface in L-ferritin assists the assembly of a functional (μ³-oxo)Tris[(μ²-peroxo)] triiron(III) cluster

After 60 min exposure to a ferrous solution, a fully assembled (μ³-oxo)Tris[(μ²-peroxo)(μ²-glutamato-κO:κO′)](glutamato-κO)(diaquo)triiron(III) anionic cluster appears in human L-ferritin.

Pozzi C. et al., Proceedings of the National Academy of Sciences 2017

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Layered metal-functionalized covalent organic frameworks as precursors of supercapacitive porous N-doped graphene

Scheme of the work showing the COF-1 structure, the metal coordination COF-1-M and the calcination process to produce N-doped graphenes. This strategy avoids the need of the use of any additional template, allowing the formation of corrugated graphene in a one-pot reaction from the COF-1–M precursors.
J. Romero. et al., J. Mater. Chem. A, 5, 4343, (2017)

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The mechanism of sliding of the human DNA clamp PCNA

X-ray crystallography: the 2.8 Å crystal structure of the human PCNA homotrimer bound to a 10 bp DNA duplex. A close-up shows the detailed interactions between the DNA phosphates (yellow spheres) and a set of positively charged residues within the PCNA central channel.
De March, M. et al., Nat.Commun. 8, 13935 (2017)

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Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins

The picture presents the structural change in NLP protein upon sugar binding: crystal structures of NLP before (blue, left) and after glucosamine binding (green, right) on the background.

Lenarčič T et al, Science, 2017, 358, pp 1431-1434
Van den Ackerveken G, Science, 2017, 358, Issue 6369, pp. 1383-1384

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How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1′ Pocket of Thermolysin

The positions of bound xenon and krypton in the crystal structure can be unambiguously identified in the electron density due to their anomalous scattering properties. Both types of noble gases populate the same position in the S₁′ cavity.

Krimmer S G et al, J. Am. Chem. Soc., 2017, 139 (30), pp 10419–10431

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Single-point mutation, metal ion concentration and low dielectric constant of the medium induce human ubiquitin aggragation

Ribbon representation of the asymmetric unit content (chains A,B and C) plus one symmetriy-related molecule of chain B (B*), of E16V crystal grown at 35 mM Zn²⁺. The metal sites (ZN1, Zn5, Zn6 and Zn7) are represented as yellow spheres. The side chain of the mutated residue (Val16) is shown as red sticks

Fermani S et al, Chem. Eur. J., 2017, 24, pp 4140

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Crystal structure of the earthworm toxin reveals the mechanism of assembly and its potential application

Crystal structure of the lysenin pore, PDB-ID 5EC5, shown in ribbons, top view. Each of the nine protomoeric units is presented in a different color.

Podobnik M. et al., Nature Communications, 7:11598 (2016)

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Nanoparticles – New light on growth mechanisms

Synchrotron X-Ray diffraction in solution is used to shed light on the growth mechanisms of the coprecipitation of iron oxide nanoparticles, showing an initial precipitation of iron hydroxide carbonate [Fe6(OH)12CO3] and ferrihydrite and the successive growth of ferrihydrite /via/ the re-dissolution of iron hydroxide carbonate to form a final magnetite phase.
LaGrow A P et al., Nanoscale, 2019,11, 6620-6628

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Extended O-Doped Polycyclic Aromatic Hydrocarbons

a) SEM images of polyaromatic molecular crystals displaying a lamellar-like texture; b) solid-state columnar π-π stacks with an interplanar distance of 3.3Å

Stassen D. et al., Angew. Chem. 2016, 128, 1 – 6

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Photosynthesis – The dark side structural proteome is now completed

The crystal structure of the phosphoribulokinase (PRK) – the last enzyme of the Calvin-Benson cycle – has been finally solved, completing its redox structural proteome. The PRK structure also allowed to shed light on the molecular evolution of PRKs in eukaryotes.

Gurrieri L. et al., Proceedings of the National Academy of Sciences Mar 2019, 201820639

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Proposal Submission - Macromolecular Crystallography

A new allocation mechanism – dedicated to macromolecular crystallography experiments – has been introduced for XRD1 starting from May 1^st 2011.
The following improvements have been implemented:
- no deadline: it is possible to submit a proposal at any time;
- proposal evaluation on a monthly basis;
- reduced dead-time between proposal submission and allocation;
- automatic re-submission in case of overbooking.
We strongly encourage MX users to take advantage of this new procedure.  It will be still possible to apply on a six-month basis only if the experiment requires a particular setup in order to be performed or  extended time is required for bureaucratic purposes such as visa applications.

Proposal Submission - Other

For experiments different than macromolecular crystallography (no perishable samples and/or particular setup required), the usual six-month based procedure should be followed (look for the User Area in the quick links). The deadlines for proposal submission for beamtime allocation are March 15th, for the period January 1st to June 30th, and September 15th, for the period July 1st to December 31th, at 4:30 pm (MET).