scholarly journals Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder

Crystals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 803 ◽  
Author(s):  
Suk-Youl Park ◽  
Hyeongju Choi ◽  
Cheolsoo Eo ◽  
Yunje Cho ◽  
Ki Hyun Nam
Keyword(s):  
Crystal Structures ◽  
Room Temperature ◽  
Sample Holder ◽  
Macromolecular Crystallography ◽  
Fixed Target ◽  
Special Equipment ◽  
Crystal Sample ◽  
X Ray ◽  
Raster Scanning ◽  
Nylon Mesh

Serial crystallography (SX) technique using synchrotron X-ray allows the visualization of room-temperature crystal structures with low-dose data collection as well as time-resolved molecular dynamics. In an SX experiment, delivery of numerous crystals for X-ray interaction, in a serial manner, is very important. Fixed-target scanning approach has the advantage of dramatically minimizing sample consumption as well as any physical damage to crystal sample, compared to other sample delivery methods. Here, we introduce the simple approach of fixed-target serial synchrotron crystallography (FT-SSX) using nylon mesh and enclosed film (NAM)-based sample holder. The NAM-based sample holder consisted of X-ray-transparent nylon-mesh and polyimide film, attached to a magnetic base. This sample holder was mounted to a goniometer head on macromolecular crystallography beamline, and translated along vertical and horizontal directions for raster scanning by the goniometer. Diffraction data were collected in two raster scanning approaches: (i) 100 ms X-ray exposure and 0.011° oscillation at each scan point and (ii) 500 ms X-ray exposure and 0.222° oscillation at each scan point. Using this approach, we determined the room-temperature crystal structures of lysozyme and glucose isomerase at 1.5–2.0 Å resolution. The sample holder produced negligible X-ray background scattering for data processing. Therefore, the new approach provided an opportunity to perform FT-SSX with high accessibility using macromolecular crystallography beamlines at synchrotron without any special equipment.

scholarly journals Polyimide mesh-based sample holder with irregular crystal mounting holes for fixed-target serial crystallography

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ki Hyun Nam ◽  
Jihan Kim ◽  
Yunje Cho
Keyword(s):  
Data Collection ◽  
Room Temperature ◽  
Picosecond Laser ◽  
Temperature Structure ◽  
Sample Holder ◽  
Fixed Target ◽  
Random Orientation ◽  
Physical Damage ◽  
Crystal Sample ◽  
Serial Crystallography

AbstractThe serial crystallography (SX) technique enables the determination of the room-temperature structure of a macromolecule while causing minimal radiation damage, as well as the visualization of the molecular dynamics by time-resolved studies. The fixed-target (FT) scanning approach is one method for SX sample delivery that minimizes sample consumption and minimizes physical damage to crystals during data collection. Settling of the crystals on the sample holder in random orientation is important for complete three dimensional data collection. To increase the random orientation of crystals on the sample holder, we developed a polyimide mesh-based sample holder with irregular crystal mounting holes for FT-SX. The polyimide mesh was fabricated using a picosecond laser. Each hole in the polyimide mesh has irregularly shaped holes because of laser thermal damage, which may cause more crystals to settle at random orientations compared to regular shaped sample holders. A crystal sample was spread onto a polyimide-mesh, and a polyimide film was added to both sides to prevent dehydration. Using this sample holder, FT-SX was performed at synchrotron and determined the room-temperature lysozyme structure at 1.65 Å. The polyimide mesh with irregularly shaped holes will allow for expanded applications in sample delivery for FT-SX experiments.

Distorted chiolite crystal structures of α-Na5M3F14 (M=Cr,Fe,Ga) studied by X-ray powder diffraction

2003 ◽  
Vol 18 (2) ◽  
pp. 128-134 ◽  
Author(s):  
A. Le Bail ◽  
A.-M. Mercier
Keyword(s):  
Crystal Structures ◽  
Powder Diffraction ◽  
Room Temperature ◽  
Rietveld Refinements ◽  
Space Group ◽  
X Ray ◽  
Precise Characterization

The crystal structures of the chiolite-related room temperature phases α-Na5M3F14 (MIII=Cr,Fe,Ga) are determined. For all of them, the space group is P21/n, Z=2; a=10.5096(3) Å, b=7.2253(2) Å, c=7.2713(2) Å, β=90.6753(7)° (M=Cr); a=10.4342(7) Å, b=7.3418(6) Å, c=7.4023(6) Å, β=90.799(5)° (M=Fe), and a=10.4052(1) Å, b=7.2251(1) Å, c=7.2689(1), β=90.6640(4)° (M=Ga). Rietveld refinements produce final RF factors 0.036, 0.033, and 0.035, and RWP factors, 0.125, 0.116, and 0.096, for MIII=Cr, Fe, and Ga, respectively. The MF6 polyhedra in the defective isolated perovskite-like layers deviate very few from perfect octahedra. Subtle octahedra tiltings lead to the symmetry decrease from the P4/mnc space group adopted by the Na5Al3F14 chiolite aristotype to the P21/n space group adopted by the title series. Facile twinning precluded till now the precise characterization of these compounds.

The crystal structures of solvent-free alkali-metal squarates from powder diffraction data

2005 ◽  
Vol 220 (11) ◽  
Author(s):  
Robert E. Dinnebier ◽  
Hanne Nuss ◽  
Martin Jansen
Keyword(s):  
High Resolution ◽  
Alkali Metal ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Room Temperature ◽  
Solvent Free ◽  
Crystallographic Data ◽  
Powder Diffraction Data ◽  
X Ray

AbstractThe crystal structures of solvent-free lithium, sodium, rubidium, and cesium squarates have been determined from high resolution synchrotron and X-ray laboratory powder patterns. Crystallographic data at room temperature of Li

Synthesis and aldol cyclotrimerization of 4,7-di-tert-butylacenaphthenone

2006 ◽  
Vol 84 (10) ◽  
pp. 1268-1272 ◽  
Author(s):  
Aaron W Amick ◽  
Keith S Griswold ◽  
Lawrence T Scott
Keyword(s):  
Key Words ◽  
Crystal Structures ◽  
Silica Gel ◽  
Room Temperature ◽  
Titanium Tetrachloride ◽  
X Ray ◽  
Synthetic Intermediates

An efficient gram scale synthesis of the previously unknown 4,7-di-tert-butylacenaphthenone (3b) is reported. The facile isomerization of epoxide 9b to ketone 3b occurs simply on stirring a solution of 9b with silica gel at room temperature. Aldol cyclotrimerization of 3b with titanium tetrachloride gives 2,5,8,11,14,17-hexa-tert-butylde cacyclene (1b) in 58% isolated yield. X-ray crystal structures have been obtained for the synthetic intermediates 4,7-di-tert-butylacenaphthene (2b) and 4,7-di-tert-butylacenaphthylene (8b).Key words: aromatic, decacyclene, hydrocarbon, nonalternant, polycyclic.

scholarly journals Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering

2016 ◽  
Vol 49 (3) ◽  
pp. 968-975 ◽  
Author(s):  
Philip Roedig ◽  
Ramona Duman ◽  
Juan Sanchez-Weatherby ◽  
Ismo Vartiainen ◽  
Anja Burkhardt ◽  
...  
Keyword(s):  
Data Collection ◽  
Room Temperature ◽  
Structural Changes ◽  
Crystalline Silicon ◽  
Background Level ◽  
Sample Holder ◽  
Macromolecular Crystallography ◽  
Recent Success ◽  
Millisecond Range ◽  
Humidified Air

Recent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose ofD1/2= 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures.

Plug-and-play polymer microfluidic chips for hydrated, room temperature, fixed-target serial crystallography

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Deepshika Gilbile ◽  
Megan L. Shelby ◽  
Artem Y. Lyubimov ◽  
Jennifer L. Wierman ◽  
Diana C. F. Monteiro ◽  
...  
Keyword(s):  
Room Temperature ◽  
Microfluidic Chips ◽  
Fixed Target ◽  
Plug And Play ◽  
X Ray ◽  
X Ray Crystallography ◽  
Serial Crystallography

This work presents our development of versatile, inexpensive, and robust polymer microfluidic chips for routine and reliable room temperature serial X-ray crystallography measurements.

Organolanthanoids. XXI Synthesis of Bis- and Tris-(diphenylphosphinocyclopenta- dienyl)lanthanoid Compounds and the X-Ray Crystal Structures of [Ln(C5H4PPh2)3(OPPh3)]·(thf)1

1997 ◽  
Vol 50 (10) ◽  
pp. 959 ◽  
Author(s):  
Glen B. Deacon ◽  
Craig M. Forsyth ◽  
Bryan M. Gatehouse ◽  
Anna Philosof ◽  
Brian W. Skelton ◽  
...  
Keyword(s):  
Oxygen Atom ◽  
Single Crystal ◽  
Crystal Structures ◽  
Room Temperature ◽  
Central Metal ◽  
Metal Oxidation ◽  
X Ray

Redox transmetallation ofTl(C5H4PPh2)with an excess of Sm in refluxing thf (thf = tetrahydrofuran) or Eu indme (dme = 1,2-dimethoxyethane) at room temperature gave thelanthanoid(II) compounds[Sm(C5H4PPh2)2](1) and[Eu(C5H4PPh2)2(dme)](2). Crystallization of (1) or[Yb(C5H4PPh2)2(dme)]with OPPh3 in dme yielded[Sm(C5H4PPh2)2(OPPh3)2](3) and[Yb(C5H4PPh2)2(OPPh3)2](4). Room-temperature transmetallation ofTl(C5H4PPh2)with Nd gave the lanthanoid(III) compound[Nd(C5H4PPh2)3(thf)](5), but analogous reactions with La, Pr, Er, Gd and Y in refluxing thfgenerally gave intractable oils, although in one instance impure[La(C5H4PPh2)3(thf)]·(thf)0 · 5,namely(6)·(thf)0 · 5, wasisolated. This complex was also obtained at room temperature by usingLaI3-activated La metal. Oxidation of (1) with 1 equiv.ofTl(C5H4PPh2)in toluene yielded solvent-freeSm(C5H4PPh2)3(7). Addition of OPPh3 to these systems allowed theisolation of[Ln(C5H4PPh2)3(OPPh3)]·(thf)x(x = 0-1 · 5; Ln = La (8), Pr (9),Nd (10), Sm (11), Er (12), Y (13)). Single-crystal X-ray structuredetermination of(10)·(thf)1 · 5,(11)·(thf)1 · 5 and(12)·(thf)1 · 5revealed formally 10-coordinate complexes with an O-bondedOPPh3, threeη5-C5H4PPh2ligands and lattice thf. The centroids of the C5 ringsand the oxygen atom surround the central metal in a distorted tetrahedralarray.

Stable sample delivery in viscous media via a capillary for serial crystallography

2020 ◽  
Vol 53 (1) ◽  
pp. 45-50 ◽  
Author(s):  
Ki Hyun Nam
Keyword(s):  
Room Temperature ◽  
Capillary Tube ◽  
Glucose Isomerase ◽  
Low Flow ◽  
Innovative Technology ◽  
Delivery Method ◽  
Crystal Sample ◽  
X Ray ◽  
Serial Crystallography ◽  
Delivery Medium

Serial crystallography (SX) is an innovative technology in structural biology that enables the visualization of the molecular dynamics of macromolecules at room temperature. SX experiments always require a considerable amount of effort to deliver a crystal sample to the X-ray interaction point continuously and reliably. Here, a sample-delivery method using a capillary and a delivery medium is introduced. The crystals embedded in the delivery medium can pass through the capillary tube, which is aligned with the X-ray beam, at very low flow rates without requiring elaborate delivery techniques, drastically reducing sample consumption. In serial millisecond crystallography using a viscous medium via a capillary, crystals of lysozyme embedded in agarose, which produce an unstable injection stream at atmospheric pressure, and crystals of glucose isomerase embedded in gelatin, which is known to be problematic for open-extruder operation, were stably delivered at a flow rate of 100 nl min−1. The room-temperature crystal structures of lysozyme and glucose isomerase were successfully determined at 1.85 and 1.70 Å resolutions, respectively. This simple but highly efficient sample-delivery method can allow researchers to deliver crystals precisely to an X-ray beam in SX experiments.

Temperature dependence of the AV3O7 (A = Ca, Sr) structure

2007 ◽  
Vol 63 (6) ◽  
pp. 836-842 ◽  
Author(s):  
Sebastian Prinz ◽  
Karine M. Sparta ◽  
Georg Roth
Keyword(s):  
Single Crystal ◽  
Temperature Dependence ◽  
Crystal Structures ◽  
Room Temperature ◽  
X Ray Diffraction ◽  
X Ray ◽  
Space Groups ◽  
Temperature Ranges ◽  
First Time

The V4+ (spin ½) oxovanadates AV3O7 (A = Ca, Sr) were synthesized and studied by means of single-crystal X-ray diffraction. The room-temperature structures of both compounds are orthorhombic and their respective space groups are Pnma and Pmmn. The previously assumed structure of SrV3O7 has been revised and the temperature dependence of both crystal structures in the temperature ranges 297–100 K and 315–100 K, respectively, is discussed for the first time.

Crystal structures of the simple monoclinic and orthorhombic polytypes of tripotassium hexacyanoferrate(III)

1978 ◽  
Vol 31 (6) ◽  
pp. 1195 ◽  
Author(s):  
BN Figgis ◽  
BW Skelton ◽  
AH White
Keyword(s):  
Single Crystal ◽  
Crystal Structures ◽  
Room Temperature ◽  
Potassium Ferricyanide ◽  
X Ray Diffraction ◽  
X Ray ◽  
Monoclinic Form

The room-temperature (295 K) crystal structures of potassium ferricyanide, K3[Fe(CN)6], have been determined for the simplest monoclinic (a reinvestigation) and orthorhombic polytypes by single- crystal X-ray diffraction. The monoclinic form is P21/c, a 7.047(3), b 10.400(3), c 8.384(3) Ǻ, β 107.29(3)°, Z 2. The iron atoms lie on special positions with symmetry 1. In the orthorhombic form, Pnca, a 13.422(6), b 10.396(4), 8.381(4) Ǻ, Z4, the iron atoms now lie on special positions with symmetry 2 (parallel to c). Residuals are 0.036 and 0.048 for 1232 and 855 'observed' reflections respectively.

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