{"title":"Texture measurements on quartz single crystals to validate coordinate systems for neutron time-of-flight texture analysis","authors":"Schmitt, M.M., Savage, D.J., Yeager, J.D., Wenk, H.-R., Lutterotti, L., Vogel, S.C.","doi":"10.1107/s1600576723009275","DOIUrl":"https://doi.org/10.1107/s1600576723009275","url":null,"abstract":"","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138535985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-15DOI: 10.1107/s1600576723008889
Munoz, P., Ilavsky, J., Newville, M., Wetter, N.U., Lourenço, R.A., Barbosa de Andrade, M., Martins, T.S., Dipold, J., Freitas, A.Z., Cides da Silva, L.C., Oliveira, C.L.P.
This study characterizes the microstructure and mineralogy of 132 (ODP sample), 1000 and 1880 million-year-old chert samples. By using ultra-small-angle X-ray scattering (USAXS), wide-angle X-ray scattering and other techniques, the preservation of organic matter (OM) in these samples is studied. The scarce microstructural data reported on chert contrast with many studies addressing porosity evolution in other sedimentary rocks. The aim of this work is to solve the distribution of OM and silica in chert by characterizing samples before and after combustion to pinpoint the OM distribution inside the porous silica matrix. The samples are predominantly composed of alpha quartz and show increasing crystallite sizes up to 33 ± 5 nm (1σ standard deviation or SD). In older samples, low water abundances (∼0.03%) suggest progressive dehydration. (U)SAXS data reveal a porous matrix that evolves over geological time, including, from younger to older samples, (1) a decreasing pore volume down to 1%, (2) greater pore sizes hosting OM, (3) decreasing specific surface area values from younger (9.3 ± 0.1 m2 g−1) to older samples (0.63 ± 0.07 m2 g−1, 1σ SD) and (4) a lower background intensity correlated to decreasing hydrogen abundances. The pore-volume distributions (PVDs) show that pores ranging from 4 to 100 nm accumulate the greater volume fraction of OM. Raman data show aromatic organic clusters up to 20 nm in older samples. Raman and PVD data suggest that OM is located mostly in mesopores. Observed structural changes, silica–OM interactions and the hydrophobicity of the OM could explain the OM preservation in chert.
{"title":"(U)SAXS characterization of porous microstructure of chert: insights into organic matter preservation","authors":"Munoz, P., Ilavsky, J., Newville, M., Wetter, N.U., Lourenço, R.A., Barbosa de Andrade, M., Martins, T.S., Dipold, J., Freitas, A.Z., Cides da Silva, L.C., Oliveira, C.L.P.","doi":"10.1107/s1600576723008889","DOIUrl":"https://doi.org/10.1107/s1600576723008889","url":null,"abstract":"This study characterizes the microstructure and mineralogy of 132 (ODP sample), 1000 and 1880 million-year-old chert samples. By using ultra-small-angle X-ray scattering (USAXS), wide-angle X-ray scattering and other techniques, the preservation of organic matter (OM) in these samples is studied. The scarce microstructural data reported on chert contrast with many studies addressing porosity evolution in other sedimentary rocks. The aim of this work is to solve the distribution of OM and silica in chert by characterizing samples before and after combustion to pinpoint the OM distribution inside the porous silica matrix. The samples are predominantly composed of alpha quartz and show increasing crystallite sizes up to 33 ± 5 nm (1σ standard deviation or SD). In older samples, low water abundances (∼0.03%) suggest progressive dehydration. (U)SAXS data reveal a porous matrix that evolves over geological time, including, from younger to older samples, (1) a decreasing pore volume down to 1%, (2) greater pore sizes hosting OM, (3) decreasing specific surface area values from younger (9.3 ± 0.1 m2 g−1) to older samples (0.63 ± 0.07 m2 g−1, 1σ SD) and (4) a lower background intensity correlated to decreasing hydrogen abundances. The pore-volume distributions (PVDs) show that pores ranging from 4 to 100 nm accumulate the greater volume fraction of OM. Raman data show aromatic organic clusters up to 20 nm in older samples. Raman and PVD data suggest that OM is located mostly in mesopores. Observed structural changes, silica–OM interactions and the hydrophobicity of the OM could explain the OM preservation in chert.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138535902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-31DOI: 10.1107/s1600576723008324
Brian R. Pauw, Glen J. Smales, Andy S. Anker, Daniel M. Balazs, Frederick L. Beyer, Ralf Bienert, Wim G. Bouwman, Ingo Breßler, Joachim Breternitz, Erik S Brok, Gary Bryant, Andrew J. Clulow, Erin R. Crater, Frédéric De Geuser, Alessandra del Giudice, Jérôme Deumer, Sabrina Disch, Shankar Dutt, Kilian Frank, Emiliano Fratini, Elliot P. Gilbert, Marc Benjamin Hahn, James Hallett, Max Hohenschutz, Martin Hollamby, Steven Huband, Jan Ilavsky, Johanna K. Jochum, Mikkel Juelsholt, Bradley W. Mansel, Paavo Penttilä, Rebecca K. Pittkowski, Giuseppe Portale, Lilo D. Pozzo, Paulo Ricardo de Abreu Furtado Garcia, Leonhard Rochels, Julian M. Rosalie, Patrick E. J. Saloga, Susanne Seibt, Andrew J. Smith, Gregory N. Smith, Venkatasamy Annadurai, Glenn A. Spiering, Tomasz M. Stawski, Olivier Taché, Andreas F. Thünemann, Kristof Toth, Andrew E. Whitten, Joachim Wuttke
A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population mean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.
{"title":"The human factor: results of a small-angle scattering data analysis round robin","authors":"Brian R. Pauw, Glen J. Smales, Andy S. Anker, Daniel M. Balazs, Frederick L. Beyer, Ralf Bienert, Wim G. Bouwman, Ingo Breßler, Joachim Breternitz, Erik S Brok, Gary Bryant, Andrew J. Clulow, Erin R. Crater, Frédéric De Geuser, Alessandra del Giudice, Jérôme Deumer, Sabrina Disch, Shankar Dutt, Kilian Frank, Emiliano Fratini, Elliot P. Gilbert, Marc Benjamin Hahn, James Hallett, Max Hohenschutz, Martin Hollamby, Steven Huband, Jan Ilavsky, Johanna K. Jochum, Mikkel Juelsholt, Bradley W. Mansel, Paavo Penttilä, Rebecca K. Pittkowski, Giuseppe Portale, Lilo D. Pozzo, Paulo Ricardo de Abreu Furtado Garcia, Leonhard Rochels, Julian M. Rosalie, Patrick E. J. Saloga, Susanne Seibt, Andrew J. Smith, Gregory N. Smith, Venkatasamy Annadurai, Glenn A. Spiering, Tomasz M. Stawski, Olivier Taché, Andreas F. Thünemann, Kristof Toth, Andrew E. Whitten, Joachim Wuttke","doi":"10.1107/s1600576723008324","DOIUrl":"https://doi.org/10.1107/s1600576723008324","url":null,"abstract":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population mean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135768827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The RootProf computer program applies multivariate model-free analysis to crystallographic data and to any x , y experimental data in general. It has been enhanced with several new features, including a graphical user interface, multithreading implementation and additional pre-processing options. The program also includes novel qualitative analysis methods, such as semiquantitative estimates derived from principal component analysis (PCA) and restrained PCA to extract the diffraction signal from active atoms. Additional quantitative analysis methods have been included, involving the combination of different datasets or the application of the standard addition method as well as tools for crystallinity analysis, kinetic analysis and extraction of free crystal cell parameters from a pair distribution function profile. The ROOT data analysis framework supports the program and can be installed on the current major platforms such as Windows, Linux and Mac OSX with detailed user documentation included. Applications of the new developments are presented and discussed in the paper, and related command files are provided as supporting information.
{"title":"New features of the <i>RootProf</i> program for model-free analysis of unidimensional profiles","authors":"Annamaria Mazzone, Mattia Lopresti, Benny Danilo Belviso, Rocco Caliandro","doi":"10.1107/s1600576723008348","DOIUrl":"https://doi.org/10.1107/s1600576723008348","url":null,"abstract":"The RootProf computer program applies multivariate model-free analysis to crystallographic data and to any x , y experimental data in general. It has been enhanced with several new features, including a graphical user interface, multithreading implementation and additional pre-processing options. The program also includes novel qualitative analysis methods, such as semiquantitative estimates derived from principal component analysis (PCA) and restrained PCA to extract the diffraction signal from active atoms. Additional quantitative analysis methods have been included, involving the combination of different datasets or the application of the standard addition method as well as tools for crystallinity analysis, kinetic analysis and extraction of free crystal cell parameters from a pair distribution function profile. The ROOT data analysis framework supports the program and can be installed on the current major platforms such as Windows, Linux and Mac OSX with detailed user documentation included. Applications of the new developments are presented and discussed in the paper, and related command files are provided as supporting information.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135617943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-20DOI: 10.1107/s1600576723008439
Richard D. Harvey, Gianluca Bello, Alexey G. Kikhney, Jaume Torres, Wahyu Surya, Christian Wölk, Chen Shen
Lipid membranes play an essential role in biology, acting as host matrices for biomolecules like proteins and facilitating their functions. Their structures and structural responses to physiologically relevant interactions ( i.e. with membrane proteins) provide key information for understanding biophysical mechanisms. Hence, there is a crucial need of methods to understand the effects of membrane host molecules on the lipid bilayer structure. Here, a purely experimental method is presented for obtaining the absolute scattering length density profile and the area per lipid of liposomal bilayers, by aiding the analysis of small-angle X-ray scattering (SAXS) data with the volume of bare headgroups obtained from grazing-incidence X-ray off-specular scattering (GIXOS) data of monolayers of the same model membrane lipid composition. The GIXOS data experimentally demonstrate that the variation of the bare headgroup volume upon change in lipid packing density is small enough to allow its usage as a reference value without knowing the lipid packing stage in a bilayer. This approach also has the advantage that the reference volume is obtained in the same aqueous environment as used for the model membrane bilayers. The validity of this method is demonstrated using several typical membrane compositions, as well as one example of a phospholipid membrane with an incorporated transmembrane peptide. This methodology allows us to obtain absolute scale rather than relative scale values using solely X-ray-based instrumentation, retaining a similar resolution to SAXS experiments. The method presented has high potential for understanding the structural effects of membrane proteins on the biomembrane structure.
{"title":"Absolute scattering length density profile of liposome bilayers obtained by SAXS combined with GIXOS: a tool to determine model biomembrane structure","authors":"Richard D. Harvey, Gianluca Bello, Alexey G. Kikhney, Jaume Torres, Wahyu Surya, Christian Wölk, Chen Shen","doi":"10.1107/s1600576723008439","DOIUrl":"https://doi.org/10.1107/s1600576723008439","url":null,"abstract":"Lipid membranes play an essential role in biology, acting as host matrices for biomolecules like proteins and facilitating their functions. Their structures and structural responses to physiologically relevant interactions ( i.e. with membrane proteins) provide key information for understanding biophysical mechanisms. Hence, there is a crucial need of methods to understand the effects of membrane host molecules on the lipid bilayer structure. Here, a purely experimental method is presented for obtaining the absolute scattering length density profile and the area per lipid of liposomal bilayers, by aiding the analysis of small-angle X-ray scattering (SAXS) data with the volume of bare headgroups obtained from grazing-incidence X-ray off-specular scattering (GIXOS) data of monolayers of the same model membrane lipid composition. The GIXOS data experimentally demonstrate that the variation of the bare headgroup volume upon change in lipid packing density is small enough to allow its usage as a reference value without knowing the lipid packing stage in a bilayer. This approach also has the advantage that the reference volume is obtained in the same aqueous environment as used for the model membrane bilayers. The validity of this method is demonstrated using several typical membrane compositions, as well as one example of a phospholipid membrane with an incorporated transmembrane peptide. This methodology allows us to obtain absolute scale rather than relative scale values using solely X-ray-based instrumentation, retaining a similar resolution to SAXS experiments. The method presented has high potential for understanding the structural effects of membrane proteins on the biomembrane structure.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135618546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-20DOI: 10.1107/s1600576723008208
Dino Aquilano, Marco Bruno, Stefano Ghignone, Linda Pastero
Calcite and aragonite are the two most abundant among the CaCO 3 polymorphs and are also well known for their rich morphology and habit, to which twinning relevantly contributes. Moreover, the calcite → aragonite transformation has been debated for a long time, even though the homo-epitaxies occurring within each polymorph have been overlooked, to date, from both experimental and theoretical points of view. Twinning is common and unfortunately can be deceptive as it can be mistaken for homo-epitaxy, thus leading to confusion regarding the growth mechanisms of many crystal aggregates. Here, experimental and theoretical studies were carried out to investigate the twinning and homo-epitaxy that operate in aragonite: (i) the connection between twinning and homo-epitaxy for contact and penetration aggregates made by the lateral {010} and {110} aragonite forms; (ii) the homo-epitaxial relationships among the {001} pinacoid and both the {010} pinacoid and the prismatic {110} aragonite forms. This work attempts to provide a new approach to monitoring the growth mechanisms of aragonite in cases where it is obtained not as a single crystal but as an aggregate. An analogous problem will be explored in our forthcoming work on calcite.
{"title":"Twinning and homoepitaxy cooperation in the already rich growth morphology of CaCO<sub>3</sub> polymorphs. I. Aragonite","authors":"Dino Aquilano, Marco Bruno, Stefano Ghignone, Linda Pastero","doi":"10.1107/s1600576723008208","DOIUrl":"https://doi.org/10.1107/s1600576723008208","url":null,"abstract":"Calcite and aragonite are the two most abundant among the CaCO 3 polymorphs and are also well known for their rich morphology and habit, to which twinning relevantly contributes. Moreover, the calcite → aragonite transformation has been debated for a long time, even though the homo-epitaxies occurring within each polymorph have been overlooked, to date, from both experimental and theoretical points of view. Twinning is common and unfortunately can be deceptive as it can be mistaken for homo-epitaxy, thus leading to confusion regarding the growth mechanisms of many crystal aggregates. Here, experimental and theoretical studies were carried out to investigate the twinning and homo-epitaxy that operate in aragonite: (i) the connection between twinning and homo-epitaxy for contact and penetration aggregates made by the lateral {010} and {110} aragonite forms; (ii) the homo-epitaxial relationships among the {001} pinacoid and both the {010} pinacoid and the prismatic {110} aragonite forms. This work attempts to provide a new approach to monitoring the growth mechanisms of aragonite in cases where it is obtained not as a single crystal but as an aggregate. An analogous problem will be explored in our forthcoming work on calcite.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135567900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-20DOI: 10.1107/s1600576723008476
Lukas Link, Rainer Niewa
Polynator is a Python program capable of identifying coordination polyhedra, molecules and other shapes in crystal structures and evaluating their distortions. Distortions are quantified by fitting the vertices of a model to a selected set of atoms. In contrast to earlier programs, models can be deformable, which allows them to represent a point group or a range of shapes such as the set of all trigonal prisms, rather than a specific, rigid shape such as the equilateral trigonal prism. The program comes with a graphical user interface and is freely available. This paper discusses its working principle and illustrates a number of applications.
{"title":"<i>Polynator</i>: a tool to identify and quantitatively evaluate polyhedra and other shapes in crystal structures","authors":"Lukas Link, Rainer Niewa","doi":"10.1107/s1600576723008476","DOIUrl":"https://doi.org/10.1107/s1600576723008476","url":null,"abstract":"Polynator is a Python program capable of identifying coordination polyhedra, molecules and other shapes in crystal structures and evaluating their distortions. Distortions are quantified by fitting the vertices of a model to a selected set of atoms. In contrast to earlier programs, models can be deformable, which allows them to represent a point group or a range of shapes such as the set of all trigonal prisms, rather than a specific, rigid shape such as the equilateral trigonal prism. The program comes with a graphical user interface and is freely available. This paper discusses its working principle and illustrates a number of applications.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135618685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-18eCollection Date: 2023-10-01DOI: 10.1107/S1600576723006428
James Birch, Tristan O C Kwan, Peter J Judge, Danny Axford, Pierre Aller, Agata Butryn, Rosana I Reis, Juan F Bada Juarez, Javier Vinals, Robin L Owen, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Tomoyuki Tanaka, Shigeki Owada, Michihiro Sugahara, So Iwata, Allen M Orville, Anthony Watts, Isabel Moraes
Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates in situ crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A2A adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.
{"title":"A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography.","authors":"James Birch, Tristan O C Kwan, Peter J Judge, Danny Axford, Pierre Aller, Agata Butryn, Rosana I Reis, Juan F Bada Juarez, Javier Vinals, Robin L Owen, Eriko Nango, Rie Tanaka, Kensuke Tono, Yasumasa Joti, Tomoyuki Tanaka, Shigeki Owada, Michihiro Sugahara, So Iwata, Allen M Orville, Anthony Watts, Isabel Moraes","doi":"10.1107/S1600576723006428","DOIUrl":"10.1107/S1600576723006428","url":null,"abstract":"<p><p>Serial crystallography has emerged as an important tool for structural studies of integral membrane proteins. The ability to collect data from micrometre-sized weakly diffracting crystals at room temperature with minimal radiation damage has opened many new opportunities in time-resolved studies and drug discovery. However, the production of integral membrane protein microcrystals in lipidic cubic phase at the desired crystal density and quantity is challenging. This paper introduces VIALS (versatile approach to high-density microcrystals in lipidic cubic phase for serial crystallography), a simple, fast and efficient method for preparing hundreds of microlitres of high-density microcrystals suitable for serial X-ray diffraction experiments at both synchrotron and free-electron laser sources. The method is also of great benefit for rational structure-based drug design as it facilitates <i>in situ</i> crystal soaking and rapid determination of many co-crystal structures. Using the VIALS approach, room-temperature structures are reported of (i) the archaerhodopsin-3 protein in its dark-adapted state and 110 ns photocycle intermediate, determined to 2.2 and 1.7 Å, respectively, and (ii) the human A<sub>2A</sub> adenosine receptor in complex with two different ligands determined to a resolution of 3.5 Å.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2023-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10543674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41132287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-01DOI: 10.1107/S1600576723004302
Denys Naumenko, Max Burian, Benedetta Marmiroli, Richard Haider, Andrea Radeticchio, Lucas Wagner, Luca Piazza, Lisa Glatt, Stefan Brandstetter, Simone Dal Zilio, Giorgio Biasiol, Heinz Amenitsch
Use of the double-gating mode implemented on the modern hybrid photon counting system EIGER2 helps to suppress the influence of beam fluctuations in pump–probe experiments at synchrotron radiation facilities and provides better data quality.
{"title":"Implication of the double-gating mode in a hybrid photon counting detector for measurements of transient heat conduction in GaAs/AlAs superlattice structures.","authors":"Denys Naumenko, Max Burian, Benedetta Marmiroli, Richard Haider, Andrea Radeticchio, Lucas Wagner, Luca Piazza, Lisa Glatt, Stefan Brandstetter, Simone Dal Zilio, Giorgio Biasiol, Heinz Amenitsch","doi":"10.1107/S1600576723004302","DOIUrl":"https://doi.org/10.1107/S1600576723004302","url":null,"abstract":"Use of the double-gating mode implemented on the modern hybrid photon counting system EIGER2 helps to suppress the influence of beam fluctuations in pump–probe experiments at synchrotron radiation facilities and provides better data quality.","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":null,"pages":null},"PeriodicalIF":6.1,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10405594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9957260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-01DOI: 10.1107/S1600576723002819
Andreas Houben, Yannick Meinerzhagen, Noah Nachtigall, Philipp Jacobs, Richard Dronskowski
The high-intensity time-of-flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM II at Garching close to Munich, Germany. Because of the world-wide 3He crisis in 2009, the authors promptly initiated the development of 3He-free detector alternatives that are tailor-made for the requirements of large-area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular- and wavelength-dependent data from the POWTEX detector, unfortunately damaged by a 50g shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the PowderReduceP2D algorithm implemented in Mantid [Arnold et al. (2014). Nucl. Instrum. Methods Phys. Res. A, 764, 156-166]. The final part of the data treatment chain, namely a novel multi-dimensional refinement using a modified version of the GSAS-II software suite [Toby & Von Dreele (2013). J. Appl. Cryst.46, 544-549], is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of GSAS-II. This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly-user sample, BaZn(NCN)2. Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi-dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the a and b lattice parameters of BaZn(NCN)2 crystallizing in Pbca as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, e.g. the two N-C-N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large-area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.
用于粉末和质地分析的高强度飞行时间(TOF)中子衍射仪POWTEX目前正在德国慕尼黑附近Garching的研究堆FRM II的东部引导大厅建造。由于2009年世界范围内的3He危机，作者迅速开始开发无3He探测器替代品，以满足大面积衍射仪的要求。兹报告2017年在美国橡树岭国家实验室散裂中子源POWGEN中子粉末衍射仪POWGEN上运行最后一个POWTEX探测器安装单元的企业。因此，本文提供了来自POWTEX探测器的第一个依赖于角度和波长的数据，不幸的是，该探测器被50g冲击损坏，但仍在运行，以及为表征传输损伤和成功重新校准体素位置而做出的努力，以便产生可靠的测量结果。还描述了使用Mantid中实现的PowderReduceP2D算法的当前数据缩减过程[Arnold et al.(2014)]。诊断。Instrum。物理方法。[j].科学通报，2004，(6):349 - 349。数据处理链的最后一部分，即使用GSAS-II软件套件的修改版本进行新的多维细化[Toby & Von Dreele(2013)]。j:。crystal .46, 544-549]与对相同事件数据的标准数据处理进行了比较，这些数据通常被简化为TOF衍射图，并用未修改版本的GSAS-II进行了细化。这包括使用POWGEN的粉末金刚石标准样品确定仪器分辨率参数，以及对友好用户样品BaZn(NCN)2进行细化。虽然在比较常规(1D)和多维(2D)处理时，每个结构参数本身看起来都很相似，但在精度方面，仔细观察会发现微小但可能显著的差异。例如，由于一维细化(0.008 Å)，在Pbca中结晶的BaZn(NCN)2的a和b晶格参数有些可疑的接近性在二维细化(0.038 Å)中不那么明显。在比较键长和键角时也发现了类似的特征，例如，两个N-C-N单元在一维结果(173°和175°)中的弯曲程度低于二维结果(167°和173°)。这一结果不仅对POWTEX具有重要意义，而且对其他具有大面积探测器的中子TOF衍射仪也具有重要意义，比如在SNS的POWGEN或未来在欧洲散裂源的DREAM光束线。
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