GM/CA@APS: A Macromolecular Crystallography Resource

GM/CA@APS：高分子晶体学资源

• 批准号: 10709870
• 负责人: ROBERT F. FISCHETTI
• 金额: $ 422.77万
• 依托单位: UCHICAGO ARGONNE, LLC
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-30 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10709870
• 关键词: 3-Dimensional; Address; Aging; Attention; Binding; Biochemistry; Cancer Etiology; Capital; Cells; Collimator; Communication; Communities; Community Outreach; Computer software; Coupled; Crystallography; DNA; Data; Data Analyses; Data Collection; Data Storage and Retrieval; Deposition; Detection; Devices; Diameter; Educational workshop; Ensure; Environment; Equipment; Failure; Feedback; Floor; Fluorescence; Friends; Funding; Goals; Immune system; Individual; Infection; Intuition; Knowledge; Laboratories; Macromolecular Complexes; Maintenance; Measures; Membrane; Methodology; Methods; Michigan; Modernization; Mutation; National Institute of General Medical Sciences; Nature; Noise; Optics; Organism; Paper; Peer Review; Performance; Periodicals; Pharmaceutical Preparations; Photons; Positioning Attribute; Preparation; Proteins; Protocols documentation; Publishing; Resolution; Resources; Robotics; Roentgen Rays; Running; Sampling; Scanning; Schedule; Schools; Science; Site; Source; Speed; Stimulus; Structure; System; Technology; Time; Training; Universities; Viscosity; Visualization; X-Ray Crystallography; beamline; cluster computing; computerized data processing; computing resources; data analysis pipeline; detector; experience; experimental study; graphical user interface; improved; instrument; instrumentation; operation; outreach; pathogen; programs; protein complex; protein structure; receptor; repaired; screening; structural biology; success; three dimensional structure; three-dimensional visualization; tool; transmission process; tumor progression; user-friendly

The primary goal of the GM/CA@APS Resource is to provide user access to cutting-edge macromolecular crystallography beamlines to determine 3-D atomic structures of forefront problems in structural biology. The Resource was founded in 1999 and has been in operation as a national user facility since 2004, providing a full array of cutting-edge technologies for macromolecular crystallography in Sector 23 at the Advanced Photon Source (APS), Argonne National Laboratory. GM/CA is led by Robert Fischetti (Argonne National Laboratory, contact PI) and Janet Smith (University of Michigan, PI) with an effective administrative structure to operate, maintain, and upgrade the beamlines, and run a high-impact user program. The GM/CA macromolecular crystallography core provides a modern, powerful environment with sophisticated tools for sample screening, interrogation and data collection in fixed-energy, SAD and MAD modes through operation of two insertion-device X-ray beamlines, 23ID-B and 23ID-D, from canted-undulator sources. The beamlines are independently tunable over a wide energy range and are built to deliver a brilliant X-ray beam with exceptionally stable position and intensity. The exceptional stability makes GM/CA an ideal facility for anomalous scattering, and users can quickly (few minutes) change energy at will within the 5.0-20 keV range (λ = 2.48 Å - 0.62 Å). The stable beam enables a powerful microcrystallography capability. Small beams for microcrystallography are created by a quad mini-beam collimator with user-selectable beam sizes of 5-, 10- and 20-micron diameter in addition to the full beam. Users can rapidly (within seconds) change beam size for any sample at any time without beam realignment. The beamlines are equipped with fast, low-noise pixel-array detectors, an Eiger 16M on 23ID-B and a Pilatus3 6M on 23ID-D. Cryo-protected samples are robotically mounted from a 288-sample Dewar and can be visualized and manipulated in the beam with micron precision. Users control the beamlines and samples with the intuitive and biologist-friendly JBluIce graphical user interface. JBluIce includes GUI-based functions for beamline control, sample centering, sample screening, data collection, X-ray fluorescence energy scan, raster scan of the sample, and data analysis. The powerful raster feature is used to scan fields of micro-crystals or to find the best diffracting region of a larger crystal. Information from raster scans can be shared with the data collection routine for a variety of data collection options. The data analysis routines provide unit cell and resolution estimates to formulate a strategy for data collection, which is automatically coupled to three data processing pipelines, providing users with feedback in near realtime. During the 2016-2018 period, a total of 857 unique individuals from 157 unique groups used GM/CA beamlines, and annually interrogated 35,000 samples, deposited 225 structures in the PDB, and published 130 papers (12% in Nature, Science, and Cell). Serial crystallography methodologies are implemented and integrated into the JBluIce automated data collection and processing pipelines for both viscous injector and fixed-target sample delivery technologies. A computing cluster and storage array network provides high-speed data storage, retrieval, backup, and realtime data processing. Users receive training from an expert staff, and can collect data on-site or remotely. The staff also contribute to a variety of community outreach activities including the annual CCP4/APS Crystallography School. A biochemistry lab provides essential capabilities for sample preparation and characterization adjacent to the beamlines. A proactive maintenance plan ensures the high level of performance and minimizes downtown. A major upgrade of beamline optics, endstation, and computing resources will prepare GM/CA for the planned 2023 arrival of a new storage ring source known as APS-U. The new optics will enable a focused, 1-micron beam, and the new source will increase brightness by 100-fold compared to the current APS. Outreach activities, user workshops, and new user training materials will prepare the user community for the opportunities and challenges of APS-U.

GM/CA@APS资源的主要目标是为用户提供访问尖端技术的途径 用大分子结晶学光束线确定三维原子结构的前沿问题 结构生物学。该资源成立于1999年，作为国家用户一直在运营 2004年建成，为大分子结晶学提供了一整套尖端技术 在阿贡国家实验室高级光子源(APS)23区。GM/CA由以下人员领导 Robert Fischetti(阿贡国家实验室，联系Pi)和Janet Smith(密歇根大学，Pi) 有一个有效的管理结构来操作、维护和升级光束线，并运行 高影响力的用户程序。GM/CA大分子结晶学核心提供了一种现代、 强大的环境，具有用于样本筛选、讯问和数据收集的复杂工具 通过操作两条插入装置X射线光束线23ID-B实现固定能量、SAD和MAD模式 和23ID-D，来自倾斜的波动子来源。光束线可以在很宽的范围内独立调节 其能量范围很广，可提供位置和强度都非常稳定的耀眼X射线束。 超乎寻常的稳定性使GM/CA成为异常散射的理想工具，用户可以快速 (几分钟)在5-20keV范围内随意改变能量(λ=2.48？-0.62？)。稳定的光束 启用强大的微晶学功能。用于微晶学的小束是由 具有用户可选的5微米、10微米和20微米直径的四路微束准直器 除了完整的横梁。用户可以快速(在几秒钟内)在任何时间更改任何样品的光束大小 没有光束重排的时间。光束线配备了快速、低噪声的像素阵列检测器， 23ID-B上的Eiger 16M和23ID-D上的Pilatus3 6M。冷冻保护的样品是机器人安装的 从288个样品的杜瓦，可以在光束中以微米级的精度可视化和操纵。 用户通过直观、生物友好的JBluIce图形用户控制光束线和样本 界面。JBluIce包括基于图形用户界面的光束线控制、样本居中、样本 筛选、数据采集、X射线荧光能量扫描、样品的栅格扫描、数据分析。 强大的栅格功能用于扫描微晶场或寻找最佳衍射区 更大的水晶。来自栅格扫描的信息可与各种数据采集例程共享 数据收集选项。数据分析例程提供单位单元格和分辨率估计 制定数据采集策略，自动耦合到三条数据处理流水线， 为用户提供近乎实时的反馈。2016-2018年期间，共有857个独一无二的 来自157个独特群体的个人使用GM/CA光束线，每年询问3.5万个样本， 在PDB中存放了225个结构，发表了130篇论文(12%发表在《自然》、《科学》和《细胞》上)。 实现了连续结晶学方法，并将其集成到JBluIce自动化数据中 用于粘性进样器和固定目标样品输送的采集和处理管道 技术。计算集群和存储阵列网络提供高速数据存储、检索 备份和实时数据处理。用户接受专家工作人员的培训，并可以收集数据 现场或远程。工作人员还为各种社区外展活动做出贡献，包括 年度CCP4/APS结晶学学校。生物化学实验室为样品提供必要的能力 与光束线相邻的制备和表征。前瞻性的维护计划可确保 高水平的性能，最大限度地减少了闹市。光束线光纤、终端站和 计算资源将使GM/CA为计划于2023年到达的已知新存储环源做好准备 作为APS-U。新的光学系统将使聚焦的1微米光束成为可能，新的光源将增加 亮度是当前APS的100倍。推广活动、用户研讨会和新用户 培训材料将使用户社区为APS-U的机遇和挑战做好准备。

项目成果

Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis.

来自热液海热菌的十二聚多铜氧化酶的晶体结构。

• DOI: 10.1107/s205979832100944x
• 发表时间: 2021
• 期刊: Acta crystallographica. Section D, Structural biology
• 作者: Paavola,JosephL;Battistin,Umberto;Ogata,CraigM;Georgiadis,MillieM
• 通讯作者: Georgiadis,MillieM

Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity.

• DOI: 10.3390/ijms22094769
• 发表时间: 2021-04-30
• 期刊: International journal of molecular sciences
• 影响因子: 5.6
• 作者: Maturana P;Orellana MS;Herrera SM;Martínez I;Figueroa M;Martínez-Oyanedel J;Castro-Fernandez V;Uribe E
• 通讯作者: Uribe E

Fast automated energy changes at synchrotron radiation beamlines equipped with transfocator or focusing mirrors.

配备转换器或聚焦镜的同步子辐射梁处的快速自动化能量变化。

• DOI: 10.1107/s1600577522001084
• 发表时间: 2022-03-01
• 期刊: Journal of synchrotron radiation
• 影响因子: 2.5
• 作者: Stepanov S;Kissick D;Makarov O;Hilgart M;Becker M;Venugopalan N;Xu S;Smith JL;Fischetti RF
• 通讯作者: Fischetti RF

New developments including X-ray standing waves in the dynamical Bragg diffraction program of X-ray Server.

新进展包括 X 射线服务器动态布拉格衍射程序中的 X 射线驻波。

• DOI: 10.1107/s160057672100830x
• 发表时间: 2021
• 期刊: Journal of applied crystallography
• 影响因子: 6.1
• 作者: Stepanov,Sergey

Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.

• DOI: 10.1002/anie.202109714
• 发表时间: 2021-10-11
• 期刊: Angewandte Chemie (International ed. in English)
• 作者: Giurgiu C;Fang Z;Aitken HRM;Kim SC;Pazienza L;Mittal S;Szostak JW
• 通讯作者: Szostak JW