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Vol. 16, No. 11 - June 2016

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Science Highlights


Applying Kβ Valence-to-Core X-ray Emission Spectroscopy to Cu(I) Binding Proteins with Relevance to Peptidylglycine Monooxygenase Reactivity  – Contacts: Serena DeBeer (Max Planck Institute / Cornell University), Ninian J. Blackburn (Oregon Health & Sciences University), Vlad Martin-Diaconescu (Universitat de Girona), Kelly Chacon (Reed College)

Protein enzymes can contain specific sites to bind copper atoms for a variety of purposes. Depending on the environment and role of the enzyme, different amino acid residues are employed to bind Cu(I).  Oxygenase enzymes employing Cu(I) often use both methionine (Met) and histidine (His) amino acids, while membrane transport proteins often use Met and not His. The identity and placement of the amino acids coordinating the Cu(I) atoms create different local environments, but it is unclear how this affects the Cu(I) atom to fulfill the role it serves for the enzyme or transporter.  A team of scientists has recently developed a new experimental approach to measure the local environmental effects on Cu(I) reactivity.  Read more...


Nucleation and Growth of Electrodeposited ZnO Visualized by in-Situ X-ray MicroscopyContact: Mary P. Ryan (Imperial College)

Zinc oxide (ZnO) is used to coat optoelectronic technology, which includes components that create and/or detect light, x-rays, infrared, or other forms of radiation. When ZnO properly crystallizes, it creates a transparent conducting film. The performance of the film is compromised when there is disruption in nucleation and growth of ZnO. A team of scientists collaborated to study the process of electrodeposition of ZnO into films.  Read more...

Workshop Summaries

SSRL 8th Annual School on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences: Theory and Application

Synchrotron-based x-ray scattering (SR-XRS) techniques offer the ability to probe nano- and atomic-scale structure that dictates the properties of advanced technological and environmental materials including organic and inorganic thin films and interfaces, nanoparticles, complex oxides, battery electrodes, polymers, minerals and poorly crystalline materials. This eighth annual School at SSRL on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences was held June 21-23, 2016 to provide a practical users’ guide for planning and conducting scattering measurements at SSRL beam lines with an emphasis on information that cannot be found in textbooks.

A total of 46 researchers, mostly graduate students and postdoctoral associates from a variety of fields, participated in this workshop. The lecture session on the first morning was devoted to introductory talks on various synchrotron scattering techniques and concepts. Afternoon talks were on surface diffraction and reflectivity, thin film diffraction, soft x-ray resonant scattering and x-ray imaging.

The second and third days provided morning sessions with talks focused on beam lines, techniques and experimental details, including data collection strategies, and data processing and analysis with sessions on SAXS reduction and analysis, area detector data reduction and analysis, reflectivity analysis, and Rietveld structure refinement. It is noteworthy that several of the leaders in these sessions were attendees of earlier schools. The afternoons of both of these days involved hands-on training at four of SSRL's beam lines (BL1-5, BL2-1, BL11-3, and BL 7-2). The first hands-on session focused on small angle scattering, reflectivity, transmission diffraction and in-situ diffraction of solution printing, while the second afternoon covered SAXS, high-resolution powder diffraction, surface diffraction and thin film scattering using area detectors.

All of the attendees of this successful workshop came away with new knowledge about how to efficiently collect, reduce, process and analyze data at SSRL’s scattering beam lines. Many thanks to the DOE, Office of Basic Energy Sciences for supporting this cross-cutting and practical workshop and to the many SSRL and Stanford postdocs and graduate students for their assistance.

Talks are available for download on the workshop website.

Macromolecular Structure Determination with Modern X-ray Crystallography Methods Course at Caltech Incorporates Beam Line 12-2

Excerpted from June 9, 2016 Phys.Org article by Lori Dajose

This spring, Caltech students had the opportunity to use x-ray - or macromolecular - crystallography to solve protein structures in a new course taught by Professor of Chemistry André Hoelz. Although the Institute has a long history in the fields of structural biology and x-ray crystallography, the chance to get hands-on experience with the technique is rare at most universities, Caltech included. Indeed, the method is more commonly performed at specialized facilities with high-energy x-ray beam lines such as SSRL. However, in 2007, thanks to a gift from the Gordon and Betty Moore Foundation, Caltech opened the Molecular Observatory—a dedicated, completely automated radiation beam line (12-2) at SSRL. "The Molecular Observatory gives us lots of beam time," notes Hoelz. "Recently, I also received a grant from the Innovation in Education Fund from the Provost's Office that was matched by the Division of Chemistry and Chemical Engineering, and this allowed me the opportunity to develop this course and train students in a way not commonly found at universities."   Read more

Organizational Change - New SSRL Electronics Systems Division

The SSRL Beam Line Electronics, the Protection Systems, and the Network Systems groups have been consolidated into the SSRL Electronics Systems Division under the leadership of Fernando Rafael. This organizational change is a follow-up to an SSRL staff survey and subsequent deliberations by an internal staff panel, which recommended integrating resources from multiple groups with broadly similar skills to enhance coverage of operational responsibilities via an enlarged and cross-trained staffing pool, and to level resource demands. Fernando brings extensive accelerator and beam line related electronics expertise as well as substantial project and personnel management experience to the new division manager role.

Upcoming Events

12th International Conference on Biology and Synchrotron Radiation - August 21-24, 2016

The International Biology and Synchrotron Radiation (BSR) meetings are held every three years with the aim of presenting and discussing state of the art applications in relevant research fields, providing a unique opportunity to discuss the novel possibilities of synchrotrons and x-ray lasers and to promote their applications to challenging biological problems.

This meeting provides a forum for scientists involved in research and development on synchrotron and free electron laser sources to come together with a broad community of biologists, with the ambition to make the best use of the most advanced infrastructures in structural biology. Possible applications range from atomic-resolution and time-resolved structures of biological macromolecules, medium resolution images of the largest molecular complexes in the living word, and cellular and sub-cellular structures.

Scientists at all career levels are invited to this meeting – ranging from graduate students, postdoctoral fellows, and principal investigators both from academia and industry. There will be ample opportunities for individual presentations.  Conference website

Save the date for the 2016 SSRL/LCLS Annual Users' Conference and Workshops, October 5-8

Organizing Committees

Plan to attend the Annual SSRL/LCLS Users' Conference and Workshops to be held at SLAC October 5-8, 2016. Contact the organizing committee to share your input on potential invited speakers. The list of tentative workshop topics follows:

  • Advanced X-ray Spectroscopy and New Approaches to and Applications of In-situ Characterization of Catalysts
  • Analysis of XFEL Scattering Data from Biomolecules and Nanoparticles
  • Electrochemical Energy Materials and Fundamental Studies Using Synchrotron X-rays
  • High Throughput Characterization of Materials and Automated Data Analysis
  • High Throughput Serial MX Data Collection at Synchrotrons and FELs
  • Hybrid Methods and Dynamics in Structural Biology
  • LCLS Data Analysis and Interface Hands-on Analysis Tutorial
  • LCLS II Instrumentation Workshops (NEH 1.x and 2.x)
  • Nonlinear X-rays - Advanced Methods and Science Applications
  • Sample Delivery: Methods & Equipment
  • SAXS for Biological Characterizations
  • Science Opportunities for Future LCLS II-HE
  • Timing and Synchronization of X-rays and Optical Lasers

Users' Conference and Workshops website

PULSE Institute 10-Year Anniversary Symposium

The PULSE Institute invites you to join in celebrating its 10-year anniversary. A symposium will be held October 8 (directly following the LCLS/SSRL User Meeting), featuring presentations on recent advances and future directions for ultrafast science. Invited speakers include: Albert Stolow, Janos Hajdu, Robert Schoenlein, Yves Acremann, Christoph Rose-Petruck, Roberto Merlin, Louis DiMauro, Robin Santra.  Registration


Call for SSRL Annual Award Nominations

August 1:  William E. and Diane M. Spicer Young Investigator Award

All SSRL users and staff are eligible for this $1,000 award honoring the professional and personal contributions that William E. and Diane M. Spicer made to our community. Submit nominations for the Spicer Young Investigator Award by August 1, including a letter of nomination summarizing the technical or scientific contributions of the candidate, the candidate's curriculum vitae and publications. Supporting letters are also encouraged.

August 15:  Melvin P. Klein Scientific Development Award

The $1,000 award honoring Melvin P. Klein's many contributions is intended to recognize outstanding research accomplishments by new investigators and to promote dissemination of research results based on work performed at SSRL. Nominations for undergraduate or graduate students, or postdoctoral fellows within three years of receiving their Ph.D., should be submitted by the August 15 deadline. The nomination package should include a letter of recommendation from the advisor as well as an abstract written by the candidate describing the SSRL-related experiments and scientific results. Candidates are encouraged to include their curriculum vitae and information on their plans to present their work at a scientific conference.

August 15: Farrel W. Lytle Award

The Farrel W. Lytle Award was established to promote important technical or scientific accomplishments in synchrotron radiation-based science and to foster collaboration and efficient use of beam time among users and staff at SSRL. SSRL users and staff are eligible to be nominated for the $1,000 Lytle Award, but only nominations for individuals will be considered (no group awards please). Submit nomination letters by August 15 including a summary of the individual's contributions and why they should be recognized through this award. Supporting letters are also encouraged.

Nomination packages for all three awards should be sent by email to the attention of Cathy Knotts. These awards will be presented during the Users' Conference Plenary Session on October 6. The awardees of the Spicer and Klein awards will be asked to give a presentation on his/her research during the Users' Conference.

User Research Administration

Proposal Deadlines

July 1, 2016 - SSRL Macromolecular Crystallography proposals (for beam time eligibility beginning fall 2016)

September 1, 2016 - SSRL X-ray/VUV Proposals (for beam time eligibility beginning in late winter 2017)

Submit proposals and beam time requests through the user portal.

Acknowledge SSRL in Your Publications

SSRL provides technical tools for world-leading science with the understanding that significant results are to be publicly disseminated. Please remember to acknowledge SSRL in ALL publications resulting from use of SSRL beam lines. This acknowledgement of SSRL is relevant even when final results are obtained at other facilities. If SSRL is not acknowledged in your paper or supplementary material, we are not able to include it on our list or report it to our funding agencies. Your assistance is essential to help us to meet our mission requirements, including assessment and reporting. More information is available on our Publications page.

The Stanford Synchrotron Radiation Lightsource (SSRL) is a third-generation light source producing extremely bright x-rays for basic and applied research.  SSRL attracts and supports scientists from around the world who use its state-of-the-art capabilities to make discoveries that benefit society. SSRL, a U.S. DOE Office of Science national user facility, is a Directorate of SLAC National Accelerator Laboratory, operated by Stanford University for the U.S. Department of Energy Office of Science.  The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences. For more information about SSRL science, operations and schedules, visit

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Questions? Comments? Contact Lisa Dunn