scholarly journals A step towards long-wavelength protein crystallography: subjecting protein crystals to a vacuum

2015 ◽  
Vol 48 (3) ◽  
pp. 913-916 ◽  
Author(s):  
Santosh Panjikar ◽  
Lars Thomsen ◽  
Kane Michael O'Donnell ◽  
Alan Riboldi-Tunnicliffe
Keyword(s):  
Data Collection ◽  
Data Quality ◽  
Crystal Lattice ◽  
Liquid Nitrogen ◽  
Proteinase K ◽  
Protein Crystals ◽  
X Ray ◽  
Long Wavelength ◽  
Flash Cooling

Using the UHV experimental endstation on the soft X-ray beamline at the Australian Synchrotron, lysozyme and proteinase K crystals have been exposed to a vacuum of 10−5 mbar, prior to flash-cooling in a bath of liquid nitrogen. Subsequent data collection on the MX2 beamline at the Australian Synchrotron demonstrated that, for lysozyme and proteinase K, it is possible to subject these mounted crystals to a vacuum pressure of 10−5 mbar without destroying the crystal lattice. Despite the lower data quality of the vacuum-pumped crystals compared with control crystals, it is demonstrated that the protein crystals can survive in a vacuum under suitable conditions.

scholarly journals The rise of neutron cryo-crystallography

2018 ◽  
Vol 74 (8) ◽  
pp. 792-799 ◽  
Author(s):  
Hanna Kwon ◽  
Patricia S. Langan ◽  
Leighton Coates ◽  
Emma L. Raven ◽  
Peter C. E. Moody
Keyword(s):  
Data Collection ◽  
Liquid Nitrogen ◽  
Room Temperature ◽  
Protein Crystallography ◽  
Protein Crystals ◽  
X Ray ◽  
Problems And Solutions ◽  
Neutron Protein Crystallography ◽  
Direct Extrapolation ◽  
Neutron Crystallography

The use of boiled-off liquid nitrogen to maintain protein crystals at 100 K during X-ray data collection has become almost universal. Applying this to neutron protein crystallography offers the opportunity to significantly broaden the scope of biochemical problems that can be addressed, although care must be taken in assuming that direct extrapolation to room temperature is always valid. Here, the history to date of neutron protein cryo-crystallography and the particular problems and solutions associated with the mounting and cryocooling of the larger crystals needed for neutron crystallography are reviewed. Finally, the outlook for further cryogenic neutron studies using existing and future neutron instrumentation is discussed.

scholarly journals Identification of the point of diminishing returns in high-multiplicity data collection for sulfur SAD phasing

2017 ◽  
Vol 24 (1) ◽  
pp. 19-28 ◽  
Author(s):  
Selina L. S. Storm ◽  
Fabio Dall'Antonia ◽  
Gleb Bourenkov ◽  
Thomas R. Schneider
Keyword(s):  
Data Collection ◽  
Data Quality ◽  
Radiation Damage ◽  
Diffraction Data ◽  
High Multiplicity ◽  
X Ray ◽  
Anomalous Data ◽  
Diminishing Returns ◽  
Sad Phasing

High-quality high-multiplicity X-ray diffraction data were collected on five different crystals of thaumatin using a homogeneous-profile X-ray beam at E = 8 keV to investigate the counteracting effects of increased multiplicity and increased radiation damage on the quality of anomalous diffraction data collected on macromolecular crystals. By comparing sulfur substructures obtained from subsets of the data selected as a function of absorbed X-ray dose with sulfur positions in the respective refined reference structures, the doses at which the highest quality of anomalous differences could be obtained were identified for the five crystals. A statistic σ{ΔF} D , calculated as the width σ of the normalized distribution of a set {ΔF} of anomalous differences collected at a dose D, is suggested as a measure of anomalous data quality as a function of dose. An empirical rule is proposed to identify the dose at which the gains in data quality due to increased multiplicity are outbalanced by the losses due to decreases in signal-to-noise as a consequence of radiation damage. Identifying this point of diminishing returns allows the optimization of the choice of data collection parameters and the selection of data to be used in subsequent crystal structure determination steps.

A simple and rapid method for mounting protein crystals at room temperature

2003 ◽  
Vol 36 (1) ◽  
pp. 165-166 ◽  
Author(s):  
Aengus Mac Sweeney ◽  
Allan D'Arcy
Keyword(s):  
Data Collection ◽  
Room Temperature ◽  
Protein Crystals ◽  
Freezing Process ◽  
Routine Method ◽  
X Ray ◽  
Significant Damage ◽  
Simplified Method ◽  
Intrinsic Quality

Cryocooling of protein crystals for X-ray data collection has now become a routine method in the majority of biostructural laboratories. The improvement of facilities at synchrotron sources and their increased use has made it essential to have properly frozen crystals for optimal data collection. Although in general crystals can be cooled without significant damage, there are often cases in which crystals with slight disorder or twinning problems suffer considerably during the freezing process. In other cases, poor or mosaic diffraction may be blamed on the cryoprotectant or cooling protocol. Many crystals may be wasted in searching for the best freezing conditions when the intrinsic quality of the crystals is poor. In principle, the collection of room-temperature diffraction data would provide a reference that would allow the detection of crystal damage caused by addition of cryoprotectant or by cryocooling. In practice, however, many investigators are reluctant to do this, one reason being that capillary mounting of crystals is a tedious method, especially for those who are new to crystallography. Here a simplified method for mounting crystals at room temperature is reported, which requires little expertise and no expensive equipment.

Recrystallization: a method to improve the quality of protein crystals

2015 ◽  
Vol 48 (3) ◽  
pp. 758-762 ◽  
Author(s):  
Hai Hou ◽  
Yue Liu ◽  
Bo Wang ◽  
Fan Jiang ◽  
Hao-Ran Tao ◽  
...  
Keyword(s):  
Crystal Quality ◽  
Proteinase K ◽  
Protein Crystals ◽  
Structural Determination ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
High Quality Protein ◽  
Before And After

The quality of protein crystals is an important parameter for structural determination with X-ray crystallography. Indeed, a prerequisite for obtaining high-resolution diffraction data is that the crystals be of sufficient quality. However, obtaining high-quality protein crystals is a well known bottleneck to protein structural determination that remains a difficult task. In this paper, it is demonstrated that recrystallization can be an effective method of improving the quality of protein crystals. Five proteins, lysozyme, proteinase K, concanavalin A, thaumatin and catalase, were used for this investigation, and the crystal quality of these proteins was examined using X-ray diffraction before and after recrystallization. Comparisons of the crystals before and after recrystallization verified that recrystallization not only enhanced the morphology of the crystals but also improved crystal quality. Therefore, it is proposed that recrystallization might be a useful alternative method for obtaining protein crystals with enhanced diffraction.

scholarly journals Thinking about police data: Analysts’ perceptions of data quality in Canadian policing

2021 ◽  
pp. 0032258X2110214
Author(s):  
Christopher D O’Connor ◽  
John Ng ◽  
Dallas Hill ◽  
Tyler Frederick
Keyword(s):  
Big Data ◽  
Data Collection ◽  
Data Quality ◽  
Research Culture ◽  
Police Services ◽  
Police Data ◽  
Data Collection And Analysis ◽  
Quality Issues

Policing is increasingly being shaped by data collection and analysis. However, we still know little about the quality of the data police services acquire and utilize. Drawing on a survey of analysts from across Canada, this article examines several data collection, analysis, and quality issues. We argue that as we move towards an era of big data policing it is imperative that police services pay more attention to the quality of the data they collect. We conclude by discussing the implications of ignoring data quality issues and the need to develop a more robust research culture in policing.

scholarly journals Protein microcrystallography using synchrotron radiation

IUCrJ ◽  
2017 ◽  
Vol 4 (5) ◽  
pp. 529-539 ◽  
Author(s):  
Masaki Yamamoto ◽  
Kunio Hirata ◽  
Keitaro Yamashita ◽  
Kazuya Hasegawa ◽  
Go Ueno ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Data Collection ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structural Features ◽  
X Ray ◽  
Data Collection Strategy ◽  
Technological Developments ◽  
Novel Method

The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as smallin mesocrystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.

A possible additional role of mineral oil in successful flash cooling

2005 ◽  
Vol 38 (6) ◽  
pp. 945-950 ◽  
Author(s):  
Lokesh Gakhar ◽  
John M. Wiencek
Keyword(s):  
Liquid Nitrogen ◽  
Nucleate Boiling ◽  
Mineral Oil ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Full Potential ◽  
Surface Cooling ◽  
Flash Cooling ◽  
Leidenfrost Temperature ◽  
Additional Role

Traditional explanations for the efficacy of mineral oil in successful flash cooling of a protein crystal correctly point to the removal of excess liquid around the crystal to prevent external ice formation. Based on the physics of the well known Leidenfrost phenomenon, an additional role that mineral oil possibly plays in aiding vitrification is suggested: that of improving cooling rates for a protein crystal plunged into liquid nitrogen. The full potential of liquid heat transfer when using liquid nitrogen is not realized in conventional cooling techniques due to film boiling that occurs around larger protein crystals. However, a thin layer of an insulating material, such as a mineral oil, around the protein crystal can prevent this vapor film from forming by raising the Leidenfrost temperature. Surface cooling then occurs in the more efficient nucleate boiling regime where liquid nitrogen is in contact with the crystal throughout the quench. Using bare and coated thermocouples, the validity of a predictive Leidenfrost temperature equation for use in liquid-nitrogen plunge cooling of protein crystals is demonstrated.

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.

scholarly journals Area Detector Systems: Setting Higher Standards for Data Quality

2014 ◽  
Vol 70 (a1) ◽  
pp. C1729-C1729
Author(s):  
Lee Daniels ◽  
Mathias Meyer
Keyword(s):  
Data Collection ◽  
Data Quality ◽  
Data Reduction ◽  
Real Life ◽  
Experimental Procedure ◽  
Area Detector ◽  
Additional Challenge ◽  
Major Factors ◽  
Data Collection Procedure

At least four major factors affect single-crystal diffraction data quality: 1) Hardware (source, goniometer and detector), 2) the sample, 3) the data collection procedure and strategy, and 4) the integration and data reduction software. Three of these factors can be carefully designed by the instrument manufacturer, and the other (the sample) can be chosen to optimize interaction with the instrument. We can define important hardware factors to allow quantification, such as absolute detectivity, overhead, readout speed, minimizing dead time and diffractometer access. Advances in area detector technology (including the new S2 generation of area detectors) and data collection approaches will be presented. The experimental procedure includes the choice of wavelength and the geometric strategy. Details of the detector operation (gain, bin-mode) can be optimized to fit the experiment. Agilent's latest CrysAlisPro software implements the 4th generation of strategy software and includes new on-the-fly detector optimization to provide significant gains in data quality. Integration software must be flexible in order to extract consistently good intensities from excellent samples and also from those that suffer from real-life flaws. Twinned samples represent an additional challenge. Agilent's new data reduction approach for twins significantly improves the data quality of both small molecule and protein twins.

Pressure-induced high-density amorphous ice in protein crystals

2008 ◽  
Vol 41 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Chae Un Kim ◽  
Yi-Fan Chen ◽  
Mark W. Tate ◽  
Sol M. Gruner
Keyword(s):  
High Pressure ◽  
Ambient Pressure ◽  
Protein Crystallization ◽  
High Density ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray ◽  
Crystallization Solution ◽  
Highly Correlated

Crystal cryocooling has been used in X-ray protein crystallography to mitigate radiation damage during diffraction data collection. However, cryocooling typically increases crystal mosaicity and often requires a time-consuming search for cryoprotectants. A recently developed high-pressure cryocooling method reduces crystal damage relative to traditional cryocooling procedures and eases or eliminates the need to screen for cryoprotectants. It has been proposed that the formation of high-density amorphous (HDA) ice within the protein crystal is responsible for the excellent diffraction quality of the high-pressure cryocooled crystals. This paper reports X-ray data that confirm the presence of HDA ice in the high-pressure cryocooled protein crystallization solution and protein crystals analyzed at ambient pressure. Diffuse scattering with a spacing characteristic of HDA ice is seen at low temperatures. This scattering then becomes characteristic successively to low-density amorphous, cubic and hexagonal ice phases as the temperature is gradually raised from 80 to 230 K, and seems to be highly correlated with the diffraction quality of crystals.

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