scholarly journals Optimizing Data Collection in the Home Lab

2014 ◽  
Vol 70 (a1) ◽  
pp. C324-C324
Author(s):  
Matthew Benning
Keyword(s):  
Membrane Proteins ◽  
Data Collection ◽  
Data Quality ◽  
Crystal Orientation ◽  
Dead Time ◽  
Biological Research ◽  
Instrument Error ◽  
X Ray ◽  
Operation Optimization ◽  
Wide Range

Many of the projects currently under investigation in biological research labs focus on macromolecules that are difficult to crystallize such as: complexes, multi-domain and membrane proteins. Typically, crystallization trials can produce small, weakly diffracting crystals that may also have other challenging attributes. Recent hardware and software developments have improved in-house data quality on a wide range of samples. Small and highly focused x-ray beams allow one to select the best diffracting portion of a larger crystal and reduce background scatter for much smaller samples. Shutterless data collection helps to reduce instrument error resulting from shutter jitter and allows fine slicing of data runs without frame to frame dead time penalties while the practice of dealing with multiple, cracked or twinned crystals has improved greatly due to software enhancements. Results from in-house data collection including: shutterless operation, optimization of crystal orientation and collection parameters will be discussed.

scholarly journals Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallography

2009 ◽  
Vol 42 (6) ◽  
pp. 1165-1175 ◽  
Author(s):  
Kazuya Hasegawa ◽  
Kunio Hirata ◽  
Tetsuya Shimizu ◽  
Nobutaka Shimizu ◽  
Takaaki Hikima ◽  
...  
Keyword(s):  
Data Collection ◽  
Dynamic Range ◽  
Protein Structures ◽  
Protein Crystallography ◽  
New Method ◽  
Oxide Semiconductor ◽  
X Ray ◽  
Rotation Method ◽  
Continuous Rotation ◽  
Wide Range

A new shutterless continuous rotation method using an X-ray complementary metal-oxide semiconductor (CMOS) detector has been developed for high-speed, precise data collection in protein crystallography. The principle of operation and the basic performance of the X-ray CMOS detector (Hamamatsu Photonics KK C10158DK) have been shown to be appropriate to the shutterless continuous rotation method. The data quality of the continuous rotation method is comparable to that of the conventional oscillation method using a CCD detector and, furthermore, the combination with fine φ slicing improves the data accuracy without increasing the data-collection time. The new method is more sensitive to diffraction intensity because of the narrow dynamic range of the CMOS detector. However, the strong diffraction spots were found to be precisely measured by recording them on successive multiple images by selecting an adequate rotation step. The new method has been used to successfully determine three protein structures by multi- and single-wavelength anomalous diffraction phasing and has thereby been proved applicable in protein crystallography. The apparatus and method may become a powerful tool at synchrotron protein crystallography beamlines with important potential across a wide range of X-ray wavelengths.

scholarly journals Applications with a brighter X-ray source and new detectors from Agilent

2014 ◽  
Vol 70 (a1) ◽  
pp. C1734-C1734
Author(s):  
Zoltan Gal ◽  
Tadeusz Skarzynski ◽  
Fraser White ◽  
Oliver Presly ◽  
Adrian Jones ◽  
...  
Keyword(s):  
Data Quality ◽  
Single Crystal ◽  
Measurement System ◽  
Single Crystal Diffraction ◽  
X Ray ◽  
Vacuum Technology ◽  
Intelligent Measurement ◽  
Wide Range

Agilent Technologies develop and supply X-ray systems for single-crystal diffraction research, including the SuperNova; a compact, highly reliable and very low maintenance instrument providing X-ray data of the highest quality; and the PX Scanner for testing and characterization of protein crystals in their original crystallization drops (in-situ). The SuperNova and PX Scanner are constantly improving, with recent enhancements including a new range of detectors using an Intelligent Measurement System. The Eos S2, Atlas S2 and Titan S2 detector range employs a smart sensitivity control of the electronic gain and is capable of instantaneously switching its binning modes thus providing unprecedented flexibility in tuning every exposure to provide the highest data quality for a wide range of experiments. We have also developed a completely new micro-focus X-ray source based on Gradient Vacuum technology, with novel filament and target designs. This novel source is an integral part of the new Agilent GV1000 X-ray diffractometer, which has been designed for applications that require even higher brightness of the X-ray beam.

scholarly journals The crystalline sponge method updated

IUCrJ ◽  
2016 ◽  
Vol 3 (2) ◽  
pp. 139-151 ◽  
Author(s):  
Manabu Hoshino ◽  
Anupam Khutia ◽  
Hongzhu Xing ◽  
Yasuhide Inokuma ◽  
Makoto Fujita
Keyword(s):  
Data Collection ◽  
Data Quality ◽  
Site Occupancy ◽  
Porous Metal ◽  
Crystallographic Analysis ◽  
Chemical Information ◽  
Benchmark Test ◽  
X Ray ◽  
Chemical Crystallography ◽  
High Site

Crystalline sponges are porous metal complexes that can absorb and orient common organic molecules in their pores and make them observable by conventional X-ray structure analysis (crystalline sponge method). In this study, all of the steps in the crystalline sponge method, including sponge crystal preparation, pore–solvent exchange, guest soaking, data collection and crystallographic analysis, are carefully examined and thoroughly optimized to provide reliable and meaningful chemical information as chemical crystallography. Major improvements in the method have been made in the guest-soaking and data-collection steps. In the soaking step, obtaining a high site occupancy of the guest is particularly important, and dominant parameters for guest soaking (e.g.temperature, time, concentration, solvents) therefore have to be optimized for every sample compound. When standard conditions do not work, a high-throughput method is useful for efficiently optimizing the soaking conditions. The X-ray experiments are also carefully re-examined. Significant improvement of the guest data quality is achieved by complete data collection at high angle regions. The appropriate disorder treatment of the most flexible ZnI2portions of the host framework and refinement of the solvents filling the remaining void are also particularly important for obtaining better data quality. A benchmark test for the crystalline sponge method toward an achiral molecule is proposed with a guaiazulene guest, in which the guest structure (with ∼ 100% site occupancy) is refined without applying any restraints or constraints. The obtained data quality withRint= 0.0279 andR1= 0.0379 is comparable with that of current conventional crystallographic analysis for small molecules. Another benchmark test for this method toward a chiral molecule is also proposed with a santonin guest. The crystallographic data obtained [Rint= 0.0421,R1= 0.0312, Flack (Parsons) = −0.0071 (11)] represents the potential ability of this method for reliable absolute structure determination.

Optimizing the spatial distribution of dose in X-ray macromolecular crystallography

2012 ◽  
Vol 20 (1) ◽  
pp. 49-57 ◽  
Author(s):  
Oliver B. Zeldin ◽  
Markus Gerstel ◽  
Elspeth F. Garman
Keyword(s):  
Spatial Distribution ◽  
Data Collection ◽  
Rotation Axis ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Crystal Shapes ◽  
Peak Dose ◽  
Wide Range ◽  
Helical Scan ◽  
Crystal Volume

X-ray data collection for macromolecular crystallography can lead to highly inhomogeneous distributions of dose within the crystal volume for cases when the crystal is larger than the beam or when the beam is non-uniform (Gaussian-like), particularly when crystal rotation is fully taken into account. Here the spatial distribution of dose is quantitatively modelled in order to compare the effectiveness of two dose-spreading data-collection protocols: helical scanning and translational collection. Their effectiveness in reducing the peak dose per unit diffraction is investigatedviasimulations for four common crystal shapes (cube, plate, long and short needles) and beams with a wide range of full width half maximum values. By inspection of the chosen metric, it is concluded that the optimum strategy is always to use as flat (top-hat) a beam as possible and to either match the beam size in both dimensions to the crystal, or to perform a helical scan with a beam which is narrow along the rotation axis and matched to the crystal size along the perpendicular axis. For crystal shapes where this is not possible, the reduction in peak dose per unit diffraction achieved through dose spreading is quantified and tabulated as a reference for experimenters.

scholarly journals XAS at the Canadian Macromolecular Crystallography Facility

2014 ◽  
Vol 70 (a1) ◽  
pp. C1525-C1525
Author(s):  
Julien Cotelesage ◽  
Pawel Grochulski ◽  
Michel Fodje ◽  
James Gorin ◽  
Kathryn Janzen ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Minimal Risk ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Biologically Relevant ◽  
Wide Range ◽  
X Ray Absorption ◽  
Do So

Recent additions to the Canadian Macromolecular Crystallography Facility have expanded the capabilities of its bending magnet beamline. It is now possible to perform x-ray absorption spectroscopy (XAS) on crystals. A wide range of biologically relevant metals can be further studied, supplementing diffraction data. XAS can be used to determine if metalloproteins are photoreducing during diffraction data collection. The geometries of metal complexes can also be inferred with near-edge and EXAFS data, often more accurately than crystallography. CMCF-BM can be employed to do the abovementioned techniques on powder and solution samples that contain a metal of interest. One XAS-based technique that shows promise is single crystal plane polarized EXAFS. This technique combines crystallographic data with the findings from XAS to yield a high resolution three dimensional atomic model. More recently a number of the procedural steps required for the acquisition of XAS-based data have been automated in the MxDC software suite. These changes to data collection make it easier for users new to these disciplines to run the XAS-based experiments. By having the necessary equipment to do XAS at a protein crystallography facility, researchers who may not have had the opportunity delve into the field of XAS now can do so with minimal risk in terms of materials, funds and time.

A new method for texture measurements using a general area detector diffraction system

2003 ◽  
Vol 18 (2) ◽  
pp. 99-102 ◽  
Author(s):  
Kurt Helming ◽  
Mike Lyubchenko ◽  
Bob He ◽  
Uwe Preckwinkel
Keyword(s):  
Data Collection ◽  
Data Quality ◽  
Pole Figure ◽  
New Method ◽  
General Area ◽  
X Ray ◽  
Area Detector ◽  
New Methods ◽  
Analysis Process ◽  
Pole Figure Data

Advances in X-ray texture solutions require new methods and descriptions for the texture analysis process, e.g., when using general area detector diffraction systems. A new method is presented that defines a general pole figure resolution and provides the possibility to optimize strategies for efficient pole figure data collection. Application of the new method improves resolution and (!) speed. New software enables simultaneous monitoring of pole and detector space. This allows a fundamentally better understanding of the collected information, e.g., in situations where peaks overlap or high backgrounds compromise data quality.

Accurate charge density data collection in under a day with a home X-ray source

2005 ◽  
Vol 38 (5) ◽  
pp. 827-829 ◽  
Author(s):  
Vladimir V. Zhurov ◽  
Elizabeth A. Zhurova ◽  
Yu-Sheng Chen ◽  
A. Alan Pinkerton
Keyword(s):  
Data Collection ◽  
Data Quality ◽  
Charge Density ◽  
Liquid Helium ◽  
High Power ◽  
Experimental Procedure ◽  
Density Data ◽  
Open Flow ◽  
X Ray ◽  
Image Plate Detector

Accurate charge density data for pentaerythritol were measured at 15 K in the laboratory in under a day using a Rigaku R-Axis Rapid high-power rotating-anode diffractometer with a curved image-plate detector, and open-flow liquid-helium cryostat. The experimental procedure and data treatment are briefly described, and data quality evaluated based on a number of criteria.

scholarly journals Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array

2015 ◽  
Vol 71 (4) ◽  
pp. 928-940 ◽  
Author(s):  
Artem Y. Lyubimov ◽  
Thomas D. Murray ◽  
Antoine Koehl ◽  
Ismail Emre Araci ◽  
Monarin Uervirojnangkoorn ◽  
...  
Keyword(s):  
Data Collection ◽  
High Efficiency ◽  
X Ray Diffraction ◽  
Delivery Methods ◽  
Still Images ◽  
X Ray ◽  
Egg White Lysozyme ◽  
Wide Range ◽  
Flash Cooling ◽  
Hen Egg White

X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.

scholarly journals EIGER detector: application in macromolecular crystallography

2016 ◽  
Vol 72 (9) ◽  
pp. 1036-1048 ◽  
Author(s):  
Arnau Casanas ◽  
Rangana Warshamanage ◽  
Aaron D. Finke ◽  
Ezequiel Panepucci ◽  
Vincent Olieric ◽  
...  
Keyword(s):  
Data Collection ◽  
Data Quality ◽  
Data Acquisition ◽  
Dead Time ◽  
Single Photon ◽  
Photon Counting ◽  
Quality Data ◽  
Macromolecular Crystallography ◽  
Single Photon Counting ◽  
Optimal Rotation

The development of single-photon-counting detectors, such as the PILATUS, has been a major recent breakthrough in macromolecular crystallography, enabling noise-free detection and novel data-acquisition modes. The new EIGER detector features a pixel size of 75 × 75 µm, frame rates of up to 3000 Hz and a dead time as low as 3.8 µs. An EIGER 1M and EIGER 16M were tested on Swiss Light Source beamlines X10SA and X06SA for their application in macromolecular crystallography. The combination of fast frame rates and a very short dead time allows high-quality data acquisition in a shorter time. The ultrafine φ-slicing data-collection method is introduced and validated and its application in finding the optimal rotation angle, a suitable rotation speed and a sufficient X-ray dose are presented. An improvement of the data quality up to slicing at one tenth of the mosaicity has been observed, which is much finer than expected based on previous findings. The influence of key data-collection parameters on data quality is discussed.

Crystal orientation and X-ray pattern prediction routines for area-detector diffractometer systems in macromolecular crystallography

1987 ◽  
Vol 20 (4) ◽  
pp. 306-315 ◽  
Author(s):  
A. Messerschmidt ◽  
J. W. Pflugrath
Keyword(s):  
Data Collection ◽  
Tilt Angle ◽  
Software Package ◽  
Crystal Orientation ◽  
Primary Beam ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
Area Detector ◽  
Detector Distance ◽  
Distance Position

Routines for crystal orientation and the prediction of expected reflections which are part of the data collection software package MADNES for area-detector diffractometer systems in macromolecular crystallography are described. This package is designed to be area-detector-system independent. In addition to refining crystal cell lengths and angles, crystal orientation, crystal-to-detector distance, position of the primary beam on the detector, and rotation of the detector around the primary beam, the orientation routine also refines the effective mosaic spread of the crystal, the beam inclination angle μand the detector tilt angle τ. A prealignment procedure is described for rapid rough orientation of the crystal. The routines are written in Fortran 77 in a modular way, so that they may be used independently of MADNES and each other.

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