scholarly journals A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
P. Roedig ◽  
I. Vartiainen ◽  
R. Duman ◽  
S. Panneerselvam ◽  
N. Stübe ◽  
...  
Keyword(s):  
Sample Holder ◽  
Macromolecular Crystallography

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.

scholarly journals All-in-one sample holder for macromolecular crystallography

2019 ◽  
Vol 75 (a2) ◽  
pp. e64-e64
Author(s):  
Christian Feiler ◽  
Dirk Wallacher ◽  
Manfred Weiss
Keyword(s):  
Sample Holder ◽  
Macromolecular Crystallography

scholarly journals PRIGo: a new multi-axis goniometer for macromolecular crystallography

2015 ◽  
Vol 22 (4) ◽  
pp. 895-900 ◽  
Author(s):  
Sandro Waltersperger ◽  
Vincent Olieric ◽  
Claude Pradervand ◽  
Wayne Glettig ◽  
Marco Salathe ◽  
...  
Keyword(s):  
Data Collection ◽  
High Precision ◽  
Optimal Strategies ◽  
Crystallographic Data ◽  
Air Bearing ◽  
Sample Holder ◽  
Macromolecular Crystallography ◽  
Parallel Kinematics ◽  
Experimental Phasing ◽  
Parallel Robotics

The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achievex, y, ztranslations and χ rotation (0–90°), followed by a φ stage (0–360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and φ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

scholarly journals Towards a compact and precise sample holder for macromolecular crystallography

2017 ◽  
Vol 73 (10) ◽  
pp. 829-840 ◽  
Author(s):  
Gergely Papp ◽  
Christopher Rossi ◽  
Robert Janocha ◽  
Clement Sorez ◽  
Marcos Lopez-Marrero ◽  
...  
Keyword(s):  
Radio Frequency Identification ◽  
Large Scale ◽  
Companion Paper ◽  
Limiting Factor ◽  
Sample Holder ◽  
Macromolecular Crystallography ◽  
Acta Cryst ◽  
Position Information ◽  
Storage Density ◽  
Sample Changer

Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines. This situation provided the motivation for the development of a compact and precise sample holder with corresponding pucks, handling tools and robotic transfer protocols. The development process included four main phases: design, prototype manufacture, testing with a robotic sample changer and validation under real conditions on a beamline. Two sample-holder designs are proposed: NewPin and miniSPINE. They share the same robot gripper and allow the storage of 36 sample holders in uni-puck footprint-style pucks, which represents 252 samples in a dry-shipping dewar commonly used in the field. The pucks are identified with human- and machine-readable codes, as well as with radio-frequency identification (RFID) tags. NewPin offers a crystal-repositioning precision of up to 10 µm but requires a specific goniometer socket. The storage density could reach 64 samples using a special puck designed for fully robotic handling. miniSPINE is less precise but uses a goniometer mount compatible with the current SPINE standard. miniSPINE is proposed for the first implementation of the new standard, since it is easier to integrate at beamlines. An upgraded version of the SPINE sample holder with a corresponding puck named SPINEplus is also proposed in order to offer a homogenous and interoperable system. The project involved several European synchrotrons and industrial companies in the fields of consumables and sample-changer robotics. Manual handling of miniSPINE was tested at different institutes using evaluation kits, and pilot beamlines are being equipped with compatible robotics for large-scale evaluation. A companion paper describes a new sample changer FlexED8 (Pappet al., 2017,Acta Cryst., D73, 841–851).

scholarly journals The complex analysis of X-ray mesh scans for macromolecular crystallography

2018 ◽  
Vol 74 (4) ◽  
pp. 355-365 ◽  
Author(s):  
Igor Melnikov ◽  
Olof Svensson ◽  
Gleb Bourenkov ◽  
Gordon Leonard ◽  
Alexander Popov
Keyword(s):  
Single Crystal ◽  
Complex Analysis ◽  
Two Dimensional ◽  
Sample Holder ◽  
Macromolecular Crystallography ◽  
Single Crystal Diffraction ◽  
X Ray ◽  
Raster Scans ◽  
Dimensional Crystal

In macromolecular crystallography, mesh (raster) scans are carried out either as part of X-ray-based crystal-centring routines or to identify positions on the sample holder from which diffraction images can be collected. Here, the methods used inMeshBest, software which automatically analyses diffraction images collected during a mesh scan and produces a two-dimensional crystal map showing estimates of the dimensions, centre positions and diffraction qualities of each crystal contained in the mesh area, are presented. Sample regions producing diffraction images resulting from the superposition of more than one crystal are also distinguished from regions with single-crystal diffraction. The applicability of the method is demonstrated using several cases.

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 FlexED8: the first member of a fast and flexible sample-changer family for macromolecular crystallography

2017 ◽  
Vol 73 (10) ◽  
pp. 841-851 ◽  
Author(s):  
Gergely Papp ◽  
Franck Felisaz ◽  
Clement Sorez ◽  
Marcos Lopez-Marrero ◽  
Robert Janocha ◽  
...  
Keyword(s):  
High Reliability ◽  
Industrial Robot ◽  
Error Recovery ◽  
Fourth Generation ◽  
Single Type ◽  
Sample Holder ◽  
Macromolecular Crystallography ◽  
Full Data ◽  
Standard Equipment ◽  
Sample Changer

Automated sample changers are now standard equipment for modern macromolecular crystallography synchrotron beamlines. Nevertheless, most are only compatible with a single type of sample holder and puck. Recent work aimed at reducing sample-handling efforts and crystal-alignment times at beamlines has resulted in a new generation of compact and precise sample holders for cryocrystallography: miniSPINE and NewPin [see the companion paper by Pappet al.(2017,Acta Cryst., D73, 829–840)]. With full data collection now possible within seconds at most advanced beamlines, and future fourth-generation synchrotron sources promising to extract data in a few tens of milliseconds, the time taken to mount and centre a sample is rate-limiting. In this context, a versatile and fast sample changer, FlexED8, has been developed that is compatible with the highly successful SPINE sample holder and with the miniSPINE and NewPin sample holders. Based on a six-axis industrial robot, FlexED8 is equipped with a tool changer and includes a novel open sample-storage dewar with a built-in ice-filtering system. With seven versatile puck slots, it can hold up to 112 SPINE sample holders in uni-pucks, or 252 miniSPINE or NewPin sample holders, with 36 samples per puck. Additionally, a double gripper, compatible with the SPINE sample holders and uni-pucks, allows a reduction in the sample-exchange time from 40 s, the typical time with a standard single gripper, to less than 5 s. Computer vision-based sample-transfer monitoring, sophisticated error handling and automatic error-recovery procedures ensure high reliability. The FlexED8 sample changer has been successfully tested under real conditions on a beamline.

Preparation of cross-sectional samples for near-surface TEM studies

1987 ◽  
Vol 45 ◽  
pp. 380-381
Author(s):  
R.C. Dickenson ◽  
K.R. Lawless
Keyword(s):  
Standard Sample ◽  
Surface Region ◽  
Specimen Preparation ◽  
Thick Sheet ◽  
Drill Bit ◽  
Sample Holder ◽  
Metal Interface ◽  
Cross Sectional ◽  
Near Surface ◽  
Cold Worked

In thermal oxidation studies, the structure of the oxide-metal interface and the near-surface region is of great importance. A technique has been developed for constructing cross-sectional samples of oxidized aluminum alloys, which reveal these regions. The specimen preparation procedure is as follows: An ultra-sonic drill is used to cut a 3mm diameter disc from a 1.0mm thick sheet of the material. The disc is mounted on a brass block with low-melting wax, and a 1.0mm hole is drilled in the disc using a #60 drill bit. The drill is positioned so that the edge of the hole is tangent to the center of the disc (Fig. 1) . The disc is removed from the mount and cleaned with acetone to remove any traces of wax. To remove the cold-worked layer from the surface of the hole, the disc is placed in a standard sample holder for a Tenupol electropolisher so that the hole is in the center of the area to be polished.

Problems with oxygen analysis in the system MgO-Al2O3-SiO2 with the electron microprobe

1992 ◽  
Vol 50 (2) ◽  
pp. 1624-1625
Author(s):  
Michel Fialin ◽  
Guy Rémond
Keyword(s):  
Transition Metal ◽  
Metal Oxides ◽  
Transition Metal Oxides ◽  
Electrostatic Charge ◽  
Carbon Layer ◽  
Sample Holder ◽  
Rock Matrix ◽  
Electrical Discharges ◽  
Thin Carbon ◽  
Beam Instabilities

Oxygen-bearing minerals are generally strong insulators (e.g. silicates), or if not (e.g. transition metal oxides), they are included within a rock matrix which electrically isolates them from the sample holder contacts. In this respect, a thin carbon layer (150 Å in our laboratory) is evaporated on the sections in order to restore the conductivity. For silicates, overestimated oxygen concentrations are usually noted when transition metal oxides are used as standards. These trends corroborate the results of Bastin and Heijligers on MgO, Al2O3 and SiO2. According to our experiments, these errors are independent of the accelerating voltage used (fig.l).Owing to the low density of preexisting defects within the Al2O3 single-crystal, no significant charge buildup occurs under irradiation at low accelerating voltage (< 10keV). As a consequence, neither beam instabilities, due to electrical discharges within the excited volume, nor losses of energy for beam electrons before striking the sample, due to the presence of the electrostatic charge-induced potential, are noted : measurements from both coated and uncoated samples give comparable results which demonstrates that the carbon coating is not the cause of the observed errors.

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