BER Structural Biology and Imaging Resources
Synchrotron, Neutron, and Cryo-EM
U.S. Department of Energy | Office of Science | Office of Biological and Environmental Research

Advanced Photon Source

DOE scientific user facility sponsored by the Office of Basic Energy Sciences

Advanced Photon Source Argonne National Laboratory

Argonne National Laboratory

The Advanced Photon Source (APS) at the U.S. Department of Energy’s Argonne National Laboratory provides ultra-bright, high-energy storage ring-generated x-ray beams for research in almost all scientific disciplines. The APS is conveniently located at Argonne National Laboratory, 30 miles southwest of Chicago, Illinois, with two nearby airports offering many travel options. The unique properties of the APS synchrotron radiation are its continuous spectrum, high flux and brightness, and high coherence, which make it an indispensable tool in the exploration of matter. The wavelengths of the emitted photons span a range of dimensions from the atomic level to biological cells, thereby providing incisive probes for advanced research in materials science, physical and chemical sciences, metrology, geosciences, environmental sciences, biosciences, medical sciences, and pharmaceutical sciences. There are three broad categories of synchrotron experimental measurement techniques available at the APS that are listed below:

  • Scattering makes use of the patterns of light produced when x-rays are deflected by the closely spaced lattice of atoms in solids and is commonly used to determine the structures of crystals and large molecules such as proteins.
  • Imaging techniques use the light-source beam to obtain pictures with fine spatial resolution of the samples under study and are used in diverse research areas such as cell biology, lithography, infrared microscopy, radiology, and x-ray tomography.
  • Spectroscopy is used to study the energies of particles that are emitted or absorbed by samples that are exposed to the light-source beam and is commonly used to determine the characteristics of chemical bonding and electron motion.

The x-ray beam is customized at each beamline to meet particular needs. With more than 60 beamlines operational, the APS offers an exceptionally broad range of experimental conditions at a single facility.

Each beamline at the APS offers a unique combination of capabilities, but some of the main considerations are energy range and tunability, special sample environments, time structures, and beam size. Specifics for each beamline and a directory of techniques can be found in the Beamlines section; however, the techniques and capabilities evolve continually. The following are some highlights.

  • The energies used range from relatively “soft” x-rays (3-5 keV) to “hard” x-rays at 100 keV and sometimes higher. At many beamlines, the energy can be tuned with relative ease.
  • Samples can be examined under extreme conditions of temperature and pressure, and several facilities are available for samples requiring special handling (e.g., biohazards, radioactive samples).
  • Many experiments involve timing, through correlation with a pulsed laser or with the time structure of the x-ray pulses, for example. In the typical operating mode, the x-rays come in evenly spaced bunches or pulses, with 0.31 mA per pulse and 11.37 nanoseconds between pulses.
  • Some beamlines employ additional optics to narrow the already tight beam into even smaller spots, offering spatial resolution into the 50-nm range.

There are a number beamlines and x-ray techniques available at the APS. The complete listing of all APS beamlines’ contacts, specifications, and status is available at the APS website. Access to these beamlines is available through the general user program.

Structural Biology Center and Advanced Protein Characterization Facility

The DOE-BER funded Structural Biology Center (SBC) is a scientific user facility for macromolecular crystallography and at Sector 19 of the Advanced Photon Source (APS). The SBC’s two beamlines – one insertion device (19-ID) and one bending magnet (19-BM) – provide highly powerful, capable and productive x-ray sources for structural biology in the US. They can deliver very low angular divergence x-ray micro-beams onto micrometer-size crystal samples mounted using a robotic systems, thereby permitting structural biologists to study the structures of large and complex molecular systems at atomic resolution. Diffraction from these crystals is recorded on large, fast, and efficient area detectors, and is processed on integrated computing systems with advanced control and data analysis software designed specifically for the SBC. The integrated robotics of sample mounting and the automation of data collection and structure determination lowers the training barrier for beamline use and allows remote access on both beamlines.

The 19-ID and 19-BM beamlines are highly efficient facilities for macromolecular crystallography covering a wide range of crystallographic projects. The SBC data demonstrate the great potential of third-generation light sources for high-throughput crystallography: (1) use of the small, brilliant undulator beam and mini-beams is highly efficient, (2) our new detector on 19-ID allows for shutter-less data acquisition for competing a data set in minutes and processing of data measured to the limit of crystal diffraction is done in near real time, (3) all aspects of the experiment, including crystal decay and the signal-to-noise ratio, can be optimized, (4) in many cases, data can be processed and structures determined using semi-automated approaches in near-real time and (5) the in situ and in cellulo data collection is available on 19-ID.

The SBC beamlines offer one of the most efficient worldwide data collection and structure determination systems currently available for protein crystallography and have continued to demonstrate record productivity – 4902 PDB deposits and 1774 unique publications.

The SBC user program is fully synchronized with the APS proposal system, and peer review process. Users requesting beamtime must complete the proposal request form and submit it electronically through the APS website. All proposals are peer-reviewed by the APS review system. Beamtime is allocated based on the project’s priority score.

The SBC accepts the following categories of proposals:

  • Standard operations — regular scheduling,
  • Standard operations — rapid access proposals,
  • Standard operations — feasibility studies,
  • Special operations — includes non-standard macromolecular crystallographic projects,
  • “Mail-in” services — SBC also offers to users “mail-in” services for data collection and structure determination.

SBC users can access the beam lines both on site and/or remotely for their experiments, structure analysis, and data backup.

Advanced Protein Characterization Facility

The Advanced Protein Characterization Facility (APCF) is a community resource available to users. This new structural biology resource is located in the Bldg. 446 (a 65,000 sq. ft. building), directly attached to Sector 19 of the APS, where SBC beamlines are located. These laboratories include:

  • Molecular Biology and Small-Scale Protein Expression
  • Bacterial, Mammalian and Insect Cell Expression
  • Protein Purification and Characterization
  • Biochemistry and Cell Biology
  • Robotic Crystallization
  • Crystal Imaging
  • BSL2 for RG2 microbial, insect and mammalian cell expression
  • Microfluidics Facility

These resources are available on cost-recovery basis and they are shared with the Midwest Center for Structural Genomics resource and Center for Structural Genomics of Infectious Diseases. The access to the APCF services is available on the cost recovery basis. The APCF uses automation and robotics for gene cloning, protein expression, protein purification, characterization and protein crystallization. The complete HTP platform and an expert team working together for over a decade was established. It delivers high quality expression clones, purified proteins and structures at low cost.

The APCF hosts eight highly integrated core-technology units:

  • Bioinformatics: target selection and construct optimization based on mining of experimental data and structure-based analysis for function prediction.
  • Robotic gene cloning: >100 cloning vectors for expression of proteins used for crystallization and protein characterization — a capacity of 20,000 constructs per year.
  • Protein expression: bacterial, insect cell and mammalian expression systems at small and large scale — a capacity of 10,000 proteins per year.
  • Semi-automated protein purification: parallel workstation systems for multiple, highly efficient large-scale purification — a capacity of 7,000 proteins per year.
  • Functional characterization: enzymatic activity, ligand binding, protein-protein/protein-nucleic interaction — a capacity of 8,000 proteins per year.
  • Crystallization: semi-automated robotic crystallization, incubation and crystal monitoring system — a capacity of 7,000 proteins per year.
  • Structure solution: semi-automated structure determination with remote access — a capacity of 1,200 data sets and ~200 structures per year.
  • Database management: all experimental data captured, stored and analyzed in the Laboratory Information Management System (LIMS).

Office space and conference rooms are available for users in Bldg 446. A conference room, several meeting rooms with teleconferencing capabilities are also available. The APCF hosts several computer clusters and has dedicated local servers for computing, databases, web application, and over 200 TB storage. Experimental data is stored in an Enterprise Oracle Database.


Andrzej Joachimiak
Structural Biology Center, director
Argonne National Laboratory
(630) 252-3926