Acta Crystallographica Section A Foundations and Advances最新文献

{"title":"Where the H is the interstitial: single-crystal neutron diffraction studies of complex metal hydrides","authors":"Christina Hoffmann, Xiaoping Wang, S. Latturner","doi":"10.1107/s2053273323099059","DOIUrl":"https://doi.org/10.1107/s2053273323099059","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"When is PXRD data good enough, or when should I stop trying to resolve those tiny peaks out of the baseline?","authors":"Matthew L. Brown","doi":"10.1107/s2053273323099254","DOIUrl":"https://doi.org/10.1107/s2053273323099254","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139361971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural genomics: past, present and future","authors":"Andrzej Joachimiak","doi":"10.1107/s2053273323098169","DOIUrl":"https://doi.org/10.1107/s2053273323098169","url":null,"abstract":"The exponential growth of genomics sequence information in the 1990s led to significant knowledge gaps in our understanding of biological systems. It was true then, and it is still true now that the sequence information bore little insights about the functions encoded in the genomes. The fi eld of Structural Genomics (SG) arose to address these gaps. The mission of SG programs was to facilitate rapid de novo structure determination for proteins representing new protein families to provide meaningful structural coverage of the genomes. There were significant challenges to advance technologies for the prepara tion of thousands of proteins and for their structural and functional characterization. The SG programs quickly addressed barriers, and deficiencies, improved effectiveness, and reproducibility, and created highly integrated and cost - effective pipelines for p rotein production and structure determination. The improvements in experimental methods developed by the SG consortia resulted in fast progress in molecular and structural biology, enhanced structure quality, and significantly benefitted biological and biomedical research, providing insights into novel structural and functional space. The experimental three - dimensional models were promptly made public through the Protein Data Bank structure repository, facilitating the structure determination of other m embers of the family, and helping to understand their molecular and biochemical functions. The light sources and dedicated macromolecular crystallography beamlines, advanced software, and computing resources have contributed to SG success and expanded biology community competence in determining protein structures. Structural biology research was set to undergo a major transformation. The advancements resulted in the determination of thousands of protein structures, mostly from unique protein families, and increased structural coverage of the rapidly expanding protein universe. These structures contributed to AlphaFold/RozeTTAFold AI algorithms allowing accurate structure prediction of millions of proteins. In principle, the original goal propo sed by the National Institutes of Health Protein Structure Initiative, that structures of all proteins should be available to the community experimentally or computationally, has been accomplished. At","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Structural Molecular Biology program at the Stanford Synchrotron Radiation Lightsource","authors":"Silvia Russi, Derek A. Mendez","doi":"10.1107/s2053273323096274","DOIUrl":"https://doi.org/10.1107/s2053273323096274","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"60 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A race against time: crystallization and characterization of berkelium and californium compounds","authors":"Thomas Albrecht-Schoenzart","doi":"10.1107/s205327332309873x","DOIUrl":"https://doi.org/10.1107/s205327332309873x","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biosynthesis of deuterated lipids for structural and biophysical characterization of biomembranes and membrane proteins","authors":"Qiu Zhang, Honghai Zhang, Matthew J Keller, Wellington Leite, Shuo Qian, Robert L Hettich, Hugh O'Neill","doi":"10.1107/s2053273323096778","DOIUrl":"https://doi.org/10.1107/s2053273323096778","url":null,"abstract":"Membrane proteins play crucial roles in many cellular processes, however, studying membrane proteins is challenging because of their complex structure and fragility when isolated from their native environment. One solution is to embed membrane proteins in a membrane-mimic to provide a more native environment to facilitate their characterization. Small-angle neutron scattering (SANS) is an ideal technique to obtain structural information on biomacromolecules under physiologically relevant conditions. With this technique, deuterated phospholipids need be used to suppress their 1H signal in SANS measurements. Currently, there are three ways to obtain deuterated phospholipids; extraction of native lipids from cells produced in deuterated media, chemical synthesis, or semi -synthetic approaches that combine both routes. In this study, we report on producing deuterated phosphatidylethanolamine (PE) by extraction and fractionation from native Escherichia coli extracts, and phosphatidylcholine (PC) from an engineered E. coli strain. The PC synthase (PCs) pathway was introduced into E. coli to produce par tially deuterated and perdeuterated PC by feeding deuterated E. coli cultures with hydrogenated or deuterated choline chloride. The isolated PC product was confirmed by 1 H Nuclear Magnetic Resonance (NMR) and Liquid Chromatography - Mass Spectrometry (LC-MS) was used to determine the deuteration level of PC produced under different growth conditions. These materials can be used for neutron scattering studies with micelles, bicelles, liposomes, styrene-maleic acid lipid particles (SMALPs), and Membrane Scaffold Protein (MSP) -based lipid nanodiscs to produce a membrane-mimicking environment for studying membrane proteins, and can be used for deuterated lipids for NMR studies as well.","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"373 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small-angle X-ray scattering applications in structural biology","authors":"L. Fan, Yun-Xing Wang","doi":"10.1107/s2053273323098133","DOIUrl":"https://doi.org/10.1107/s2053273323098133","url":null,"abstract":"Small-angle X - ray scattering (SAXS) is a complementary technique to Macromolecular Crystallography, NMR and Cryo -EM techniques and is becoming more widely used in structural biology. Crystallography requires good crystals and NMR has a size limitation. Cryo - EM studies biomolecules under a frozen condition. SAXS, on the other hand, allows for the study of the structure and dynamics of macrobiomolecules and their complexes in solution and under various buffer conditions such as salt concentration, pH, with or without ligand as well as under changing sample environments such as temperature and pressure. SAXS provides insight not only into global information about size and shape of biomacrobiomolecules, but also the information about flexibility and an ensemble of conformers. SAXS data can also be used in tandem with other biophysical methods (including crystallography, NMR, AFM and cryo-EM) by providing additional restraints that further improve simulations, validate structural models as well as fi nd missing fragments. The SAXS Facility of the Natio nal Cancer Institute (NCI) opens to all intramural and extramural research communities. The mission of the SAXS Core Facility is to provide support to the user communities with expertise in experimental design, data collection, processing, analysis, and in terpretation. The research fi eld includes but is not limited to structural studies of nucleic acids, proteins, protein assemblies, virus particles, lipid membranes and membrane-protein/DNA complexes. This presentation gives a brief introduction to the NCI SAXS facility and highlights recent scientific achievements in structural biology produced by NCI SAXS core users. NCI SAXS Core website: https://ccr.cancer.gov/center - for -structural-biology/saxs-core-facility","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"What to do when h, k and l do not describe all the reflections in the diffraction?","authors":"Jessica Bruhn","doi":"10.1107/s2053273323097206","DOIUrl":"https://doi.org/10.1107/s2053273323097206","url":null,"abstract":"Here I will present a recently determined crystal structure of ipragliflozin L - proline, a pharmaceutical drug used for the treatment of type 2 diabetes. Due to the small crystal size, MicroED was used to determine this structure. Initial phasing was carried out in the orthorhombic space group P 212121, but refinement in this space group proved to be challenging. Subsequent reduction in symmetry to P 21 produced a structure that could be refined","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"118 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate crystal structures of ices from X-ray and ED with Hirshfeld atom refinement","authors":"K. Woźniak, M. Chodkiewicz, R. Gajda, V. Prakapenka, Przemyslaw Dera","doi":"10.1107/s2053273323098108","DOIUrl":"https://doi.org/10.1107/s2053273323098108","url":null,"abstract":"Background. Water is an essential chemical compound for living organisms, and twenty of its different crystal solid forms (ices) are known. Still, there are many fundamental problems with these structures such as establishing the correct positions and thermal motions of hydrogen atoms. The list of ice structures is not yet complete as DFT calculations and spectroscopic measurements have suggested existence for additional as of yet unknown phases. In many ice structures, neither neutron diffraction nor DFT calculations nor X - ray diffraction methods can easily solve the problem of hydrogen atom disorder or accurately determine their atomic displacement parameters. Methods. We applied a new way of refinement of single crystal high pressure X - ray synchrotron and laboratory X -ray and electron diffraction data called Hirshfeld Atom Refinement. This method utilizes aspherical atomic scattering factors (X - rays), and aspherical atomic electrostatic potentials (ED), based on so called stockholder (Hirshfeld) partition and is especially effective in the case of refinement of crystals of H -rich compounds. Results. Here we present accurate crystal structures of H2O, D2O and mixed (50%H2O/50%D2O) ice VI and ice VII obtained by Hirshfeld Atom Refinement (HAR) against high pressure single crystal synchrotron and laboratory X - ray diffraction data as well as results of refinement of hexagonal ice obtained by HAR against electron diffraction data. It was possible to obtain O - H bond lengths and anisotropic atomic displacement parameters for disordered hydrogen atoms which are in good agreement with the corresponding results of single crystal neutron diffraction data.[1] Conclusions. Our results show that Hirshfeld atom refinement against X - ray diffraction and electron diffraction data is a tool which can","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"2013 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unsolvable Rh₂ <i>L</i> ₄.2NCR structures","authors":"Sandy Eagle, Alain M. Beauparlant","doi":"10.1107/s2053273323096900","DOIUrl":"https://doi.org/10.1107/s2053273323096900","url":null,"abstract":"","PeriodicalId":6903,"journal":{"name":"Acta Crystallographica Section A Foundations and Advances","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139362110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}