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Xiao Q, Wu T, Bao K, Tang J, Zhang Y, Zhang W, Zhu Z, Gu Y, Zhou S, Li C, Lu L, Jiang L, Liu Y, Qin W. Upgrade of crystallography beamline BL19U1 at the Shanghai Synchrotron Radiation Facility. J Appl Crystallogr 2024; 57:630-637. [PMID: 38846766 PMCID: PMC11151664 DOI: 10.1107/s1600576724002188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/07/2024] [Indexed: 06/09/2024] Open
Abstract
BL19U1, an energy-tunable protein complex crystallography beamline at the Shanghai Synchrotron Radiation Facility, has emerged as one of the most productive MX beamlines since opening to the public in July 2015. As of October 2023, it has contributed to over 2000 protein structures deposited in the Protein Data Bank (PDB), resulting in the publication of more than 1000 scientific papers. In response to increasing interest in structure-based drug design utilizing X-ray crystallography for fragment library screening, enhancements have been implemented in both hardware and data collection systems on the beamline to optimize efficiency. Hardware upgrades include the transition from MD2 to MD2S for the diffractometer, alongside the installation of a humidity controller featuring a rapid nozzle exchanger. This allows users to opt for either low-temperature or room-temperature data collection modes. The control system has been upgraded from Blu-Ice to MXCuBE3, which supports website-mode data collection, providing enhanced compatibility and easy expansion with new features. An automated data processing pipeline has also been developed to offer users real-time feedback on data quality.
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Affiliation(s)
- Qingjie Xiao
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Tingting Wu
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Kangwen Bao
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Jianchao Tang
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Yupu Zhang
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Weizhe Zhang
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Zhongjie Zhu
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Yijun Gu
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Shuyu Zhou
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Chunyu Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Lanlu Lu
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Luozhen Jiang
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Yang Liu
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, People’s Republic of China
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Snell EH, Helliwell JR. Microgravity as an environment for macromolecular crystallization – an outlook in the era of space stations and commercial space flight. CRYSTALLOGR REV 2021. [DOI: 10.1080/0889311x.2021.1900833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- E. H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA
- Materials Design and Innovation Department, SUNY Buffalo, Buffalo, NY, USA
| | - J. R. Helliwell
- Chemistry Department, University of Manchester, Manchester, UK
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Abstract
In this review, we describe how the interplay among science, technology and community interests contributed to the evolution of four structural biology data resources. We present the method by which data deposited by scientists are prepared for worldwide distribution, and argue that data archiving in a trusted repository must be an integral part of any scientific investigation.
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Affiliation(s)
- Helen M. Berman
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
| | - Catherine L. Lawson
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
| | - Brinda Vallat
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
| | - Margaret J. Gabanyi
- Center for Integrative Proteomics Research, Institute for Quantitative Biomedicine, Department of Chemistry and Chemical Biology, 174 Frelinghuysen Road, Piscataway New Jersey 08854
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Michalska K, Tan K, Chang C, Li H, Hatzos-Skintges C, Molitsky M, Alkire R, Joachimiak A. In situ X-ray data collection and structure phasing of protein crystals at Structural Biology Center 19-ID. JOURNAL OF SYNCHROTRON RADIATION 2015; 22:1386-95. [PMID: 26524303 PMCID: PMC4629866 DOI: 10.1107/s1600577515016598] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/05/2015] [Indexed: 05/22/2023]
Abstract
A prototype of a 96-well plate scanner for in situ data collection has been developed at the Structural Biology Center (SBC) beamline 19-ID, located at the Advanced Photon Source, USA. The applicability of this instrument for protein crystal diffraction screening and data collection at ambient temperature has been demonstrated. Several different protein crystals, including selenium-labeled, were used for data collection and successful SAD phasing. Without the common procedure of crystal handling and subsequent cryo-cooling for data collection at T = 100 K, crystals in a crystallization buffer show remarkably low mosaicity (<0.1°) until deterioration by radiation damage occurs. Data presented here show that cryo-cooling can cause some unexpected structural changes. Based on the results of this study, the integration of the plate scanner into the 19-ID end-station with automated controls is being prepared. With improvement of hardware and software, in situ data collection will become available for the SBC user program including remote access.
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Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Kemin Tan
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Changsoo Chang
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Hui Li
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
| | | | - Michael Molitsky
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Randy Alkire
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, USA
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Gifford LK, Carter LG, Gabanyi MJ, Berman HM, Adams PD. The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2012; 13:57-62. [PMID: 22527514 PMCID: PMC3588887 DOI: 10.1007/s10969-012-9133-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 03/05/2012] [Indexed: 02/01/2023]
Abstract
The Technology Portal of the Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB; http://technology.sbkb.org/portal/ ) is a web resource providing information about methods and tools that can be used to relieve bottlenecks in many areas of protein production and structural biology research. Several useful features are available on the web site, including multiple ways to search the database of over 250 technological advances, a link to videos of methods on YouTube, and access to a technology forum where scientists can connect, ask questions, get news, and develop collaborations. The Technology Portal is a component of the PSI SBKB ( http://sbkb.org ), which presents integrated genomic, structural, and functional information for all protein sequence targets selected by the Protein Structure Initiative. Created in collaboration with the Nature Publishing Group, the SBKB offers an array of resources for structural biologists, such as a research library, editorials about new research advances, a featured biological system each month, and a functional sleuth for searching protein structures of unknown function. An overview of the various features and examples of user searches highlight the information, tools, and avenues for scientific interaction available through the Technology Portal.
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Affiliation(s)
- Lida K. Gifford
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | | | - Margaret J. Gabanyi
- Department of Chemistry & Chemical Biology, Rutgers – The State University of New Jersey, Piscataway, NJ 08854
| | - Helen M. Berman
- Department of Chemistry & Chemical Biology, Rutgers – The State University of New Jersey, Piscataway, NJ 08854
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
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Cohen AE, Ellis PJ, Miller MD, Deacon AM, Phizackerley RP. An automated system to mount cryo-cooled protein crystals on a synchrotron beam line, using compact sample cassettes and a small-scale robot. J Appl Crystallogr 2002; 35:720-726. [PMID: 24899734 PMCID: PMC4041710 DOI: 10.1107/s0021889802016709] [Citation(s) in RCA: 220] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2002] [Accepted: 09/13/2002] [Indexed: 11/10/2022] Open
Abstract
An automated system for mounting and dismounting pre-frozen crystals has been implemented at the Stanford Synchrotron Radiation Laboratory (SSRL). It is based on a small industrial robot and compact cylindrical cassettes, each holding up to 96 crystals mounted on Hampton Research sample pins. For easy shipping and storage, the cassette fits inside several popular dry-shippers and long-term storage Dewars. A dispensing Dewar holds up to three cassettes in liquid nitrogen adjacent to the beam line goniometer. The robot uses a permanent magnet tool to extract samples from, and insert samples into a cassette, and a cryo-tong tool to transfer them to and from the beam line goniometer. The system is simple, with few moving parts, reliable in operation and convenient to use.
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Affiliation(s)
- Aina E. Cohen
- Stanford Synchrotron Radiation Laboratory, SLAC, MS 69, 2575 Sand Hill Road, Menlo Park, 94025-7015, USA
| | - Paul J. Ellis
- Stanford Synchrotron Radiation Laboratory, SLAC, MS 69, 2575 Sand Hill Road, Menlo Park, 94025-7015, USA
| | - Mitchell D. Miller
- Stanford Synchrotron Radiation Laboratory, SLAC, MS 69, 2575 Sand Hill Road, Menlo Park, 94025-7015, USA
| | - Ashley M. Deacon
- Stanford Synchrotron Radiation Laboratory, SLAC, MS 69, 2575 Sand Hill Road, Menlo Park, 94025-7015, USA
| | - R. Paul Phizackerley
- Stanford Synchrotron Radiation Laboratory, SLAC, MS 69, 2575 Sand Hill Road, Menlo Park, 94025-7015, USA
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