scholarly journals RoboDiff: combining a sample changer and goniometer for highly automated macromolecular crystallography experiments

2016 ◽  
Vol 72 (8) ◽  
pp. 966-975 ◽  
Author(s):  
Didier Nurizzo ◽  
Matthew W. Bowler ◽  
Hugo Caserotto ◽  
Fabien Dobias ◽  
Thierry Giraud ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
High Capacity ◽  
High Accuracy ◽  
Macromolecular Crystallography ◽  
Sample Changer ◽  
High Level

Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection. This aim has been achieved using a high level of diagnostics at all steps of the process from mounting and characterization to data collection. The RoboDiff has been in service on the fully automated endstation MASSIF-1 at the ESRF since September 2014 and, at the time of writing, has processed more than 20 000 samples completely automatically.

scholarly journals A tutorial for learning and teaching macromolecular crystallography

2008 ◽  
Vol 41 (6) ◽  
pp. 1161-1172 ◽  
Author(s):  
Annette Faust ◽  
Santosh Panjikar ◽  
Uwe Mueller ◽  
Venkataraman Parthasarathy ◽  
Andrea Schmidt ◽  
...  
Keyword(s):  
Data Collection ◽  
Data Processing ◽  
Diffraction Data ◽  
Structure Determination ◽  
Macromolecular Crystallography ◽  
Data Set ◽  
Learning And Teaching

Five experiments have been designed to be used for teaching macromolecular crystallography. The three proteins used in this tutorial are all commercially available; they can be easily and reproducibly crystallized and mounted for diffraction data collection. For each of the five experiments the raw images and the processed data of a sample diffraction data set as well as the refined coordinates and phases are provided for teaching the steps of data processing and structure determination.

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.

scholarly journals Visualization of protein crystals by high-energy phase-contrast X-ray imaging

2019 ◽  
Vol 75 (11) ◽  
pp. 947-958 ◽  
Author(s):  
Maxim Polikarpov ◽  
Gleb Bourenkov ◽  
Irina Snigireva ◽  
Anatoly Snigirev ◽  
Sophie Zimmermann ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Collection ◽  
Diffraction Data ◽  
Phase Contrast ◽  
High Energy ◽  
Protein Crystals ◽  
Cubic Phase ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
X Ray Imaging

For the extraction of the best possible X-ray diffraction data from macromolecular crystals, accurate positioning of the crystals with respect to the X-ray beam is crucial. In addition, information about the shape and internal defects of crystals allows the optimization of data-collection strategies. Here, it is demonstrated that the X-ray beam available on the macromolecular crystallography beamline P14 at the high-brilliance synchrotron-radiation source PETRA III at DESY, Hamburg, Germany can be used for high-energy phase-contrast microtomography of protein crystals mounted in an optically opaque lipidic cubic phase matrix. Three-dimensional tomograms have been obtained at X-ray doses that are substantially smaller and on time scales that are substantially shorter than those used for diffraction-scanning approaches that display protein crystals at micrometre resolution. Adding a compound refractive lens as an objective to the imaging setup, two-dimensional imaging at sub-micrometre resolution has been achieved. All experiments were performed on a standard macromolecular crystallography beamline and are compatible with standard diffraction data-collection workflows and apparatus. Phase-contrast X-ray imaging of macromolecular crystals could find wide application at existing and upcoming low-emittance synchrotron-radiation sources.

scholarly journals Visualisation of membrane protein crystals using X-ray imaging

2014 ◽  
Vol 70 (a1) ◽  
pp. C351-C351
Author(s):  
Anna Warren ◽  
Wes Armour ◽  
Danny Axford ◽  
Mark Basham ◽  
Thomas Connolley ◽  
...  
Keyword(s):  
Data Collection ◽  
Diffraction Data ◽  
Cubic Phase ◽  
Informed Decision Making ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Shape Estimation ◽  
X Ray ◽  
Raster Scanning ◽  
X Ray Imaging

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallise on much smaller scales and are frequently mounted in opaque or highly refractive materials.[1,2] It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this poster the use of X-ray microradiography and microtomography is reported as a tool for crystal visualisation, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals, and crystals mounted in opaque materials such as lipidic cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to a diffraction grid scan. However, for sample location and shape estimation alone, just a few radiographic projections may be required; hence reducing the dose the crystals will be exposed to prior to the diffraction data collection.[3]

scholarly journals Radiation damage in macromolecular crystallography: what is it and why should we care?

2010 ◽  
Vol 66 (4) ◽  
pp. 339-351 ◽  
Author(s):  
Elspeth F. Garman
Keyword(s):  
Data Collection ◽  
Data Quality ◽  
Radiation Damage ◽  
Current Literature ◽  
Diffraction Data ◽  
Absorbed Dose ◽  
Macromolecular Crystallography ◽  
Physical Processes ◽  
Quality Degradation ◽  
The Subject

Radiation damage inflicted during diffraction data collection in macromolecular crystallography has re-emerged in the last decade as a major experimental and computational challenge, as even for crystals held at 100 K it can result in severe data-quality degradation and the appearance in solved structures of artefacts which affect biological interpretations. Here, the observable symptoms and basic physical processes involved in radiation damage are described and the concept of absorbed dose as the basic metric against which to monitor the experimentally observed changes is outlined. Investigations into radiation damage in macromolecular crystallography are ongoing and the number of studies is rapidly increasing. The current literature on the subject is compiled as a resource for the interested researcher.

TrimethylamineN-oxide as a versatile cryoprotective agent in macromolecular crystallography

2011 ◽  
Vol 44 (2) ◽  
pp. 433-436 ◽  
Author(s):  
Christoph Mueller-Dieckmann ◽  
Brice Kauffmann ◽  
Manfred S. Weiss
Keyword(s):  
Data Collection ◽  
Radiation Damage ◽  
Diffraction Data ◽  
Test Cases ◽  
Third Generation ◽  
Diffraction Experiment ◽  
Macromolecular Crystallography ◽  
Cryoprotective Agents ◽  
The Past ◽  
Effects Of Radiation

The surge of macromolecular crystallography is intimately linked to the advent of methods for cryoprotecting macromolecular crystals. Only if crystals are kept cold during data collection can they withstand the effects of radiation damage during a diffraction experiment, especially at third-generation synchrotron sources. While a number of different cryoprotective agents and procedures have been described in the literature over the past three decades, it is still a time- and crystal-consuming process to establish and optimize a good cryo-condition for a specific crystal. In this study, trimethylamineN-oxide (TMAO) has been identified as a very versatile cryoprotectant for macromolecular crystals. In a few test cases it was shown that diffraction data collected from crystals treated with TMAO are of very good quality.

Detection of twinning in macromolecular crystallography

2016 ◽  
Vol 231 (10) ◽  
Author(s):  
Zhipu Luo ◽  
Zbigniew Dauter
Keyword(s):  
Data Collection ◽  
Diffraction Pattern ◽  
Crystal Structures ◽  
Protein Data Bank ◽  
Diffraction Data ◽  
Data Bank ◽  
Statistical Properties ◽  
Macromolecular Crystallography ◽  
Atomic Models

AbstractThe merohedrally or pseudo-merohedrally twinned crystals cannot be identified during diffraction pattern inspection at the stage of data collection. Several methods for identifying twinning and estimating the twin fraction are suitable for macromolecular crystals, and all are based on the statistical properties of the measured diffraction intensities. They can be based on either the overall statistical properties of the measured reflection intensities or on the comparison of reflection intensities related by the twinning operation. The application of various tests for identification of twinning and estimation of twinning fraction is discussed, with examples of diffraction data from the Protein Data Bank. Twinning makes the solution of crystal structures more difficult, but once initially solved, the atomic models can be properly refined by the existing programs.

UPAYA MENINGKATKAN KOMPETENSI GURU SMP DALAM MENYUSUN TES HASIL BELAJAR BERBASIS KETERAMPILAN BERPIKIR KRITIS MELALUI SUPERVISI AKADEMIK

2019 ◽  
Vol 3 (4) ◽  
pp. 772
Author(s):  
Leni Suryani
Keyword(s):  
Critical Thinking ◽  
Data Collection ◽  
Learning Outcomes ◽  
Student Learning Outcomes ◽  
Thinking Skills ◽  
Critical Thinking Skills ◽  
Teacher Competence ◽  
Collection Data ◽  
High Level ◽  
Teacher Data

This research is motivated by the competence of teachers in preparing poor learning outcomes tests and has not been able to measure high-level thinking skills, especially critical thinking skills. Therefore the researcher seeks to improve teacher competence in compiling tests on student learning outcomes based on critical thinking skills through academic supervision. This study uses a school action research design that has stages of planning, implementation, observation, and reflection. This research was conducted for 2 months starting April 9 to May 17, 2019 for Physics teachers in the 7 target schools. Data is sourced from interviews with teachers and test documents prepared by the teacher. Data collection techniques include observation, interviews and documentation. Data analysis through the stages of data collection, data simplification, data presentation, conclusion drawing. Data were analyzed using assessment rubrics adjusted to indicators of critical thinking skills. The results of this study conclude that teacher competence in preparing tests of learning outcomes based on critical thinking skills has increased from the first cycle with a percentage of 61% with sufficient categories to 76% with good categories in cycle II.

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