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最先进的 大分子晶体学光束线，以确定三维原子结构的前沿问题， 结构生物学The Resource成立于1999年，一直作为全国用户运营 自2004年以来，该设施为大分子晶体学提供了一系列尖端技术 在阿贡国家实验室的先进光子源（APS）的23区。GM/CA由 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，并运行一个 高影响力的用户程序。GM/CA大分子晶体学核心提供了一个现代， 强大的环境，具有用于样品筛选、询问和数据收集的复杂工具， 通过操作两个插入器械X射线束线23 ID-B实现固定能量、SAD和MAD模式 和23 ID-D，来自倾斜波荡器源。光束线在宽范围内可独立调谐。 能量范围，并建立提供一个辉煌的X射线束具有非常稳定的位置和强度。 异常的稳定性使GM/CA成为异常散射的理想工具，用户可以快速地 (few分钟）在5.0-20 keV范围内（λ = 2.48 kJ- 0.62 kJ）随意改变能量。稳定梁 使其具有强大的微晶体学能力。用于微晶体学的小光束是由 四通道微型光束准直器，用户可选择5微米、10微米和20微米直径的光束尺寸， 除了全梁。用户可以快速（在几秒钟内）改变任何样品的光束大小， 没有光束重新对准的时间。光束线配备了快速、低噪声的像素阵列探测器， 23 ID-B上的Eiger 16 M和23 ID-D上的Pilatus 36 M。冷冻保护样品由机器人安装 从288样品杜瓦瓶，可以可视化和微米精度的光束操纵。 用户通过直观且生物学家友好的JBluIce图形用户控制光束线和样品 接口. JBluIce包括基于GUI的功能，用于光束线控制、样品居中、样品 筛选、数据收集、X射线荧光能量扫描、样品的光栅扫描和数据分析。 强大的光栅功能可用于扫描微晶体的场或找到最佳衍射区域， 更大的水晶来自光栅扫描的信息可以与数据收集例程共享，用于各种 数据收集选项。数据分析例程提供单位单元和分辨率估计， 制定数据收集策略，该策略自动耦合到三个数据处理管道， 为用户提供近乎实时的反馈。在2016-2018年期间，共有857个独特的 来自157个独特群体的个体使用GM/CA光束线，每年询问35，000个样本， 在PDB上存放了225个结构，发表了130篇论文（12%在Nature，Science和Cell上）。 实施系列晶体学方法并将其集成到JBluIce自动化数据中 用于粘性注射器和固定目标样品输送的收集和处理管道 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。用户接受专家人员的培训，并可以收集数据 现场或远程。工作人员还参与各种社区外展活动，包括 每年的CCP 4/APS晶体学学校。生物化学实验室提供了基本的能力， 在光束线附近进行制备和表征。主动维护计划可确保 高水平的性能和最大限度地减少市中心。光束线光学系统、终端站和 计算资源将为GM/CA准备计划在2023年到来的新存储环源， APS-U新的光学器件将使一个集中，1微米的光束，新的来源将增加 亮度比目前的APS提高了100倍。外联活动、用户研讨会和新用户 培训材料将使用户群体做好准备，迎接APS-U的机遇和挑战。

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