Remote Access Facilities: What, Where & How?

Conference: 2020: 70th ACA Annual Meeting
08/03/2020: 12:00 PM  - 3:00 PM 
1.2.1 
Education Session 
Virtual  

Presentations

Remote Opener: Breaking Barriers to Crystallization Using Remote Crystal Growth Screening and Imaging

12:00 PM - 12:20 PM 
The vast majority of biomolecular structural information is derived from macromolecular X-ray crystallography methods, which serve as a foundation for structural biology and account for nearly 90% of the more than 165,000 biomolecular structures available in the PDB. Crystallography requires high-quality, well-diffracting crystals; coaxing biomolecules into crystalline form is a rate-limiting step in structure determination. Searching for conditions in which a biomolecule will crystallize often entails screening multiple different constructs against thousands of crystallization conditions, requiring large sample amounts and many person-hours in a typical laboratory set-up. In recent circumstances due to the COVID-19 pandemic, being physically in the laboratory for setting up crystallization screening has become even more difficult. The Crystallization Center at HWI has been in continuous operation as a crystallization resource for 20 years providing mail-in crystallization and remote access to crystal growth monitoring. These services have become even more critical in the face of restrictions due to COVID-19. The Crystallization Center is a high-throughput facility that provides expertise and access to state-of-the-art instrumentation to facilitate efficient and cost-effective crystallization. We have extensive robotics for automated sample handling with very small sample volumes integrated with advanced imaging and a Formulatrix Rock Imager with SONICC for rapid detection of crystal growth. The current pipeline in the Crystallization Center screens for 1,536 conditions in one experimental plate and employs a robust imaging schedule, all of which is then accessible remotely. Here, we will present details about the current capacity for high-throughput crystal growth screening. We will also discuss innovations we are developing and opportunities for enhanced crystallization services that will further facilitate crystallization for biomolecular structure determination, including scale up and optimization, in situ diffraction experiments and enhanced imaging for crystal detection. 

View Proposal 430

Author

Sarah Bowman, Hauptman-Woodward Medical Research Institute Buffalo, NY 

Socially-distanced Crystallography in the time of COVID: Remote capabilities at SSRL

12:20 PM - 12:40 PM 
The SSRL Structural Molecular Biology group operates 5 protein crystallography (PX) beam lines on the SPEAR3 storage ring, BL7-1, BL9-2, BL12-1, BL12-2 and BL14-1. All of the PX beam lines are MAD-capable, with one station (BL7-1) using a single-crystal side-scattering monochromator with a limited energy range (typically 3000-4000 eV), and the other four using liquid nitrogen-cooled double crystal monochromators giving a much wider energy range capability (over 10000 eV). Two of the beamlines (BL12-1 and BL12-2) are in-vacuum undulator microfocus beamlines ideal for collecting data from small crystals. The SSRL PX beam lines are fully automated, with samples being mounted by the Stanford Automated Mounting system (SAM) from either Uni-Pucks or SSRL 96-port cassettes. Data collection is controlled with the Blu-Ice/DCS software system. Images collected during sample screening are automatically analyzed and processed, and the results, including the number of spots, Bravis lattice, unit cell, estimated mosaicity and resolution, are visible almost immediately through Blu-Ice, and also via the internet through Web-Ice. In the mid-2000s, the SSRL PX beamlines became the first in the world to offer fully remote access to users, who connected to the beam line computers via the highly responsive NX client. Since the ultimate goal of synchrotron data collection is to get the best possible data from the best available crystals, the combination of high-throughput automation and remote access at SSRL revolutionized the way in which scientists interacted with synchrotron beam lines to achieve this goal. In this past experimental run, our fully evolved remote access capability meant that we were able to open the SSRL PX beamlines for critical COVID-19 related research. 

View Proposal 437

Author

Jennifer Wierman, SLAC/Stanford University Palo Alto, CA 

Additional Author

Clyde Smith, SSRL/SLAC Menlo Park, CA 

Serial Electron Diffraction for Proteins and Small Molecules

12:40 PM - 1:00 PM 
Serial crystallography, where diffraction snapshots of a large ensemble of randomly oriented crystals are taken, evades the cumulative damage inherent to rotation diffraction techniques. This approach has facilitated the use of sub-micron crystals in latest-generation X-ray sources, making large classes of small, radiation-sensitive systems such as recalcitrant protein nano-crystals or nano-porous materials amenable to crystallographic structure solution. We recently demonstrated a new scheme for dose-fractionated serial electron nano-crystallography in a scanning TEM, which combines the benefits of serial crystallography with the favorable scattering properties of electrons. It can be conducted in standard microscopes in a highly automated manner and without requiring specific sample delivery devices [1]. I will present our data collection and processing pipeline, show results from protein and small-molecule crystals, and discuss specific advantages and challenges of a serial crystallography approach as compared to conventional rotation techniques for different types of samples. [1] R. Bücker, P. Hogan-Lamarre, P. Mehrabi, E. C. Schulz, L. A. Bultema, Y. Gevorkov, W. Brehm, O. Yefanov, D. Oberthür, G. H. Kassier, and R. J. D. Miller, Nat. Commun. 11, 996 (2020). 

View Proposal 297

Author

Robert Bücker, Max Planck Institute for the Structure and Dynamics of Matter Hamburg

Additional Author(s)

Pascal Hogan-Lamarre, University of Toronto Toronto
Pedram Mehrabi, Max Planck Institute for the Structure and Dynamics of Matter Hamburg
Eike C. Schulz, Max Planck Institute for the Structure and Dynamics of Matter Hamburg
Günther H. Kassier, Max Planck Institute for the Structure and Dynamics of Matter Hamburg
R. J. Dwayne Miller, University of Toronto Toronto, Ontario 

Coffee Break

1:00 PM - 1:20 PM 

Advancing Structure-Based Drug Design: IMCA-CAT Responds to Emerging Needs of the Pharmaceutical Industry

1:20 PM - 1:40 PM 
For over 20 years, the Industrial Macromolecular Crystallography Association Collaborative Access Team (IMCA-CAT) has focused exclusively on accelerating drug discovery and development by delivering synchrotron-based diffraction data. Rapid turnaround of high quality and low-cost structural data is essential in ensuring success in structure-based drug design and an increasing number of computer-aided drug design projects. Today, IMCA-CAT operates a state-of-the-art MX beamline; operating continuously with fully unattended data collection for overnight means that >90% of samples are turned around within one day. IMCA-CAT can handle crystals in a variety of pins and pucks, the data are automatically processed and then rapidly delivered to researchers in a secure, encrypted, and reliable software framework. In addition to MX data collection, IMCA-CAT serves as the conduit for SAXS data collection and structure-based consultancy services. On the horizon are modes of access to Hauptman-Woodward Medical Research Institute's centers for high-throughput crystallization screening, cryo-EM structure determination, and microcrystal electron diffraction. IMCA-CAT is the one-stop shop for all the services that the next generation pharmaceutical structural biologist will need. Opportunities abound for researchers in all pharmaceutical and biotechnology organizations to access IMCA-CAT for structural services. 

View Proposal 436

Author

Jesse Yoder, IMCA-CAT Lemont, IL 

Additional Author(s)

Anne M. Mulichak, IMCA-CAT / Hauptman Woodward Research Institute Lemont, IL 
J. Lewis Muir, IMCA-CAT / Hauptman Woodward Research Institute Lemont, IL 
Eric Zoellner, IMCA-CAT / Hauptman Woodward Research Institute Lemont, IL 
Joe Digilio, IMCA-CAT / Hauptman Woodward Research Institute Lemont, IL 
Erica Duguid, IMCA-CAT / Hauptman Woodward Research Institute Lemont, IL 
Lisa Keefe, IMCA-CAT / HWI @ Advanced Photon Source, Argonne National Lab

The SER-CAT Virtual Beamline: Providing light when YOU need it in your home lab

1:40 PM - 2:00 PM 
Since 1999, SER-CAT has been working towards the concept of providing its members with a "Virtual Beamline, which could be integrated into their daily workflow much like your X-ray lab down the hall. SER-CAT beamlines 22ID and 22BM were designed and built for remote operation, we began investigating robotic crystal mounting automation in 2000 with Oceaneering Space Systems. In 2003, a highly modified Berkeley ALS Automounter was installed on 22BM. Using 22BM as a user-based testbed, the beamline and experiment control interface SERGUI was continually modified until a reliable, robust and user-friendly system achieved. In 2006, the SER-CAT Virtual Beamline came online providing remote crystal screening and data collection capability on both 22ID (capacity 430 crystals) and 22BM (capacity 96 crystals). The Virtual Beamline includes software integration as well. The SERGUI beam line control interface allows the remote user full control of the beamline from their home lab including beamline/goniometer optimization, wavelength selection, fluorescence scans, automatic crystal centering and rastering, automated crystal screening and MAD/SAD/Helical data collection. Today over 95% of SER-CAT members routinely collect data remotely. To assist remote users in the efficient use of their beamtime, SER-CAT has implemented 12-hour shifts with 16-hours/day on-site user support. Multiple Access Time (MAT) shifts have also been made available to SER-CAT members for fast turn-around and flexible data collection capabilities. SER-CAT also provides its members access to on-the-fly automated data processing using XDS, KYLIN and DIALS. HKL2000, XDS, MOSFLM, and DIALS are also available for manual data processing. All users' data can be remotely, quickly, reliably and securely downloaded from SER-CAT Globus/GridFTP archive server to users' home systems anywhere and anytime. An overview of SER-CAT's Remote Access Program including robotics, beamline/experiment control and automated data processing and structure determination will be described and discussed. Work supported by the SER-CAT Member Institutions, University of Georgia Research Foundation, The National Institutes of Health (S10_RR25528 and S10_RR028976) and the Georgia Research Alliance. 

View Proposal 379

Author

Zhongmin Jin, SER-CAT/University of Georgia Argonne, IL 

Additional Author(s)

John Gonczy, SER-CAT/University of Georgia Argonne, IL 
James Fait, SER-CAT BMB, UGA
Zheng-qing "Albert" Fu, SER-CAT/University of Georgia Argonne, IL 
John Chrzas, SER-CAT/University of Georgia Argonne, IL 
John Rose, SER-CAT/University of Georgia Athens, GA 
Bi-Cheng Wang, University of Georgia

Development of an Alternative Approach to Time-Resolved X-ray Crystallography

2:00 PM - 2:20 PM 
Development of X-ray free electron laser sources (XFELs) and methods for serial crystallography have driven major advances in time-resolved (TR) protein crystallography. TR-crystallography is a wonderful tool for understanding protein dynamics and catalysis, allowing much greater understanding of structural motions and intermediate states in proteins. Early TR work was largely limited to proteins whose conformational changes could be triggered optically using an intrinsic chromophore, and whose motions were reversible in the crystal, so that a single crystal could be pumped and reset multiple times to generate the diffraction data. Serial crystallography using microcrystals has enabled non-reversible motions to be observed by utilizing large amounts of sample and getting one diffraction image per crystal. These experiments wouldn't have been possible without the extraordinary brightness of XFELs and the newest generation of synchrotron sources. More recently, serial crystallography has incorporated chemical triggering via diffusion on millisecond timescales, short enough to reveal biologically important intermediate states. However, the barrier to entry for current optically or chemically triggered TR crystallography techniques at XFELs and synchrotrons is high. Very large numbers of similar size and morphology crystals must be generated. Optical excitation and/or crystal mixing and delivery systems are complex and must be integrated into the beamline. Fine tuning for a given protein crystal system and efficient serial data collection using these methods requires multiple collaborators, knowledgeable beamline staff, and often large amounts of instrument time at the very few available beamlines suited to these experiments. This complexity puts TR crystallography beyond the reach of most investigators in the wider structural biology community. Alternative methods are needed to allow TR crystallography to be exploited fully by the field. Ideally, these methods should require far fewer crystals, allow data collection from standard MX beamlines without need for special sample delivery apparatus, and allow multiple routes to reaction initiation. We have been developing an alternative method to time-resolved serial crystallography that decouples the sample preparation and reaction evolution times from the data collection time, allows both optical and chemical triggering, and requires only remote data collection at standard synchrotron beamlines. Here we present preliminary data for our new TR-crystallography technique. 

View Proposal 193

Author

Jonathan Clinger, Cornell University Ithaca, NY 

Additional Author(s)

David Moreau, Cornell University Ithaca, NY 
Robert Thorne, Physics Dept, Cornell Univ

Sub-100 Microsecond Time Resolved SAXS at BioCAT

2:20 PM - 2:40 PM 
Time resolved SAXS (TR-SAXS) allows the measurement of kinetic intermediates after an initiating event. The BioCAT beamline (Sector 18) at the Advanced Photon Source uses chaotic and laminar flow microfluidic mixers to measure time ranges from ~80 µs to 1.5 s. Recent advances include: new mixer designs to optimize accessible time ranges and sample consumption; improved microbeam focusing and mixer fabrication techniques to reduce parasitic scattering; improved positioning and exposure triggering for optimal reliability; and a new, easy to use GUI for controlling all aspects of the experiments. These advances have significantly improved data quality and ease of use. Time resolved experiments can now be done with as little as ~200 µL of sample at modest concentrations for slow (>100 ms) reactions, whereas ultra-fast time resolved measurements can be done with as little as ~1 mL of sample. The TR-SAXS program at BioCAT is open to general users. 

View Proposal 174

Author

Jesse Hopkins, BioCAT (Sector 18, APS), Illinois Institute of Technology Downers Grove, IL 

Additional Author(s)

Thomas Irving, Biology, Illinois Inst of Technology Chicago, IL 
Srinivas Chakravarthy, BioCAT (Sector 18, APS), Illinois Institute of Technology Argonne, IL 

Science at a distance: the CHESS experience

2:40 PM - 3:00 PM 
MacCHESS has supported remote operation at a macromolecular crystallography (MX) station, and mail-in operation at a BioSAXS station, at CHESS (the Cornell High Energy Synchrotron Source) for years. Now, restrictions due to COVID-19 have required rethinking of modes of operation, not only for MX and BioSAXS, but for all stations at CHESS. This poster reports on developments made for operation in June 2020, and those planned for the October 2020 run. Critical factors for successful experiments include: • Recognition that setup time may be longer than under previous conditions • Use of multiple communication modes • Detailed scheduling of activities, coordinating with other stations • Contingency planning in case of equipment failure or personnel non-availability We anticipate that remote and mail-in modes of operation will be available for most experiments at every station, saving on travel expenses as well as allowing convenient collaboration between multiple experimenters. 

View Proposal 434

Author

Doletha Szebenyi, MacCHESS, Cornell Univ Ithaca, NY 

Additional Author(s)

Richard Gillilan, MacCHESS, Cornell Univ Ithaca, NY 
Aaron Finke, Cornell University Groton, NY