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SSRL Headlines Vol. 10, No. 4  October, 2009


Contents of this Issue:

  1. Science Highlight — Researchers Visualize the Structural Intermediates of the Nickel-catalyzed Enzyme that Makes Methane
  2. SSRL User Operations Resume
  3. SSRL/LCLS Users' Meeting and Workshops Wrap-up
  4. Symposium Celebrates SSRL Pioneer
  5. SSRL Users' Organization Executive Committee Election Results
  6. Researchers Reconstruct Complete Protein Network
  7. Herman Winick Awarded Andrei Sakharov Prize for Upholding Human Rights
  8. Submit X-ray/VUV Beam Time Requests by November 15
  9. Upcoming X-ray, VUV and Macromolecular Crystallography Proposal Deadline
  10. Former SSRL Colleague will be Missed
  11. Please Report SSRL-Related Papers, Invited Talks, and Awards

1.  Science Highlight — Researchers Visualize the Structural Intermediates of the Nickel-catalyzed Enzyme that Makes Methane
       (contact: R. Sarangi,

highlight figure
In the atmosphere, methane is a much more potent greenhouse gas than carbon dioxide, trapping 20 times more heat. As a fuel, methane burns cleanly, producing less carbon dioxide per unit of heat than other fuels. For these reasons, understanding methane production is immediately important.

All of the biologically produced methane comes from methanogenic archaea bacteria. These methanogens produce methane using an enzyme called methyl-coenzyme M reductase. MCR's complex reaction requires a reduced nickel cofactor in the enzyme's active site. Researchers have proposed two competing theories of the enzyme's mechanism that differ in the chemistry of the first step of the reaction.

A group of researchers led by SSRL's Ritimukta Sarangi used Beam Line 9-3 to acquire structural information for the MCR's reaction intermediates to determine which mechanistic theory is correct. Overcoming difficulties due to MCR's sensitivity to oxygen, the researchers used a combination of Ni K-edge x-ray absorption spectroscopic (XAS) studies and density functional theory (DFT) calculations to find the electronic and geometric properties of various enzyme-intermediate complexes.

Through these experiments, the researchers identified which of the proposed mechanistic theories is correct. They also found that certain traits of the nickel cofactor help stabilize the potentially unstable reaction intermediates. This work was published in the April issue of the journal Biochemistry.

To learn more about this research see the full scientific highlight.

2.   SSRL User Operations Resume       

User Operations resumed at SSRL this week following our annual three-month shutdown period. The shutdown was carefully orchestrated to complete concurrent and tightly scheduled back-to-back projects both safely and on time. Our thanks to the many people who have worked tremendously hard to ensure the success of these updates to the SPEAR3 storage ring, the beam lines and the facility in general.

A test of 200 milliamp operations occurred during the final two weeks of the FY2009 experimental run and we have approval to continue operating at that current during the fall portion of our FY2010 run. To further our goal of achieving an optimal blend of higher current, beam stability and quality user data, tests will be conducted at currents up to 500 milliamps during scheduled accelerator physics periods this fall when SSRL users are not collecting data. During these AP periods, SSRL staff will characterize beam line performance and run experiments with control samples to better understand any changes that occur as the intensity is increased. At the same time, Radiation Protection staff will conduct careful radiological surveys of the beam line shielding to ensure safe operations at the elevated current.

In the words of SSRL Acting Director Piero Pianetta, "With the completion of the SPEAR3 Beam Line Upgrade project in 2009, we are back to our full complement of 25 fully operational beam lines with two more that will be brought into operation during the coming year. These additional beam lines will enable us to increase the number of users who can to perform science at SSRL and help alleviate some of the oversubscription rates that we have been experiencing over the past several years.

The large number of users who will cycle through SSRL on a daily basis to conduct more than 500 experiments during the first scheduling period alone, present a challenge to ensure that the work is properly planned and that hazards are identified and mitigated. Starting this past year, we have worked to improve the SSRL user processes to make sure they are well aligned to Work Planning and Control. For the coming run we will implement a process that will provide additional pre-run oversight to our users in an effort to help identify any hazards that might have otherwise slipped through the cracks. In addition, we have added personal protective equipment, or PPE, stations at strategic places around the lab and at each beam line so that safety glasses, gloves, sharps containers etc. are readily available.

I am looking forward to a safe and productive run in FY2010 as well as working hard with users and staff to identify opportunities that will bring new and exciting programs to the laboratory".

see operating and beam line schedules at:

4.   SSRL/LCLS Users' Meeting and Workshops Wrap-up
       excerpted from SLAC Today article by Lauren Knoche

The SSRL/LCLS Users' Meeting and Workshops wrapped up on Thursday, October 22. More than 250 participants from around the world attended the activities over the 5-day event, which updated users on facility capabilities and performance at SLAC, highlighting 35 years of fantastic research at the Stanford Synchrotron Radiation Lightsource, the start of commissioning-with-user science at Linac Coherent Light Source and the importance of user safety while using SLAC x-ray facilities.

"The SSRL/LCLS Users' Meeting and Workshops is a way to get users to come together and talk about what they are doing," said SLAC physicist Sebastien Boutet, one of the program chairs for the event.

The event launched with a pre-meeting symposium on Sunday, October 18, "Advances in Lightsource Science-Past, Present and Future," in honor of SLAC Photon Science and Stanford Applied Physics Professor Sebastian Doniach, who served as the founding Director of the Stanford Synchrotron Radiation Lightsource (then called the Stanford Synchrotron Radiation Project). Thirty-five years later, SSRL continues to produce fantastic results (see article 4 below).

After the Monday morning overview talks, the presentations moved to more specific presentations by SSRL and LCLS users. "The scientific talks are highlights of what users have achieved during the past year," said SSRL Senior Staff Scientist and meeting co-organizer Donghui Lu. Two such talks were given by Yulin Chen, who at the meeting received the Spicer Award for his work in material sciences on topological insulators; and Leslie Jimison who accepted the Klein Award for her materials science research on semiconducting polymers.

highlight figure
Mike Toney
The Farrel Lytle Award was presented on Monday night to SSRL Senior Staff Scientist Mike Toney. The prize aims to foster collaboration between SSRL users and staff, and recognizes an individual who has made significant technical or scientific contributions in synchrotron radiation-based science. Mike Toney received the award for his outstanding support of user science programs and innovation in the use of x-ray scattering in organic thin films and other energy-related materials. Although he was not able to attend in person, Farrel Lytle sent a letter congratulating Mike.

Congratulations as well to Michael Blank, Yingge Wang, Leili Baghaei Rad, Inna Vishik and Raymond Sierra on their award-winning poster contributions to the graduate student poster competition held as part of the event. Abstracts for their respective posters can be viewed at:

see also SLAC Today article at:

4.   Symposium Celebrates SSRL Pioneer
       SLAC Today Article by Nicholas Bock

highlight figure
Seb Doniach
The Stanford Synchrotron Radiation Lightsource and Linac Coherent Light Source Users' Meeting and Workshops got started a day early this year, with more than 100 students and scientists spending Sunday at Kavli Auditorium to celebrate the 75th birthday of SLAC Photon Science and Stanford Applied Physics Professor Sebastian Doniach.

Doniach was one of the key players in adapting SLAC's SPEAR ring for use as a light source, and from 1973 to 1977 served as the first Director of SSRL. According to the event organizer, Prof. Aharon Kapitulnik, Stanford, Doniach also made important contributions in condensed matter physics, superconductors and biophysics.

The symposium, titled "Advances in Light Source Science-Past, Present and Future," covered a similarly wide range of topics. Nine presenters from around the world gave talks on everything from the Doniach Phase Diagram-an important model in condensed matter physics-to the role of physics in biology and medicine.

"Seb is a real pioneer," Kapitulnik said. "The symposium provided a great opportunity to honor him."

5.   SSRL Users' Organization Executive Committee Election Results

The SSRL Users' Organization Executive Committee (SSRLUOEC) met on October 20 immediately following the annual Users' Meeting. Newly elected representatives to the 2009-10 SSRLUOEC were announced during the Tuesday morning session by incoming chair Katherine Kantardjieff (CSU Fullerton) and again at the SSRLUOEC meeting for anyone who may have missed the earlier announcement. New members include: Junko Yano (LBNL) representing Bio Spectroscopy/Bio SAXS; David Singer (UC Berkeley/LBNL) for Environmental/Geoscience; Matthew Sazinsky (Pomona College) for Macromolecular Crystallography; Aaron Lindenberg (Stanford University) for Ultrafast Science; R. Joseph Kline (NIST) for Materials Science and Leslie Jimison (Stanford University) as a graduate student representative. The next SSRLUOEC meeting will be scheduled soon and users are invited to participate to discuss any issues or suggestions they have. Information on SSRLUOEC members and activities are posted at:

6.   Researchers Reconstruct Complete Protein Network
       SLAC Today Article by Nicholas Bock

Researchers at the Stanford Synchrotron Radiation Lightsource have helped resolve the structures of 73 proteins involved in the metabolic processes of Thermotoga maritima, a heat-loving bacterium found in deep-sea thermal vents. The work is part of a larger study conducted by the Joint Center for Structural Genomics and collaborators to reconstruct the organism's central metabolic network-a complex system that encompasses more than 478 different proteins. Published in the September 18 issue of Science, the study is the most comprehensive of its kind ever completed. The results could help explain how metabolic networks evolve, and could help drive further research in both medicine and energy science.

After screening the samples, researchers used the SSRL protein crystallography beam to create x-ray diffraction patterns of the crystallized proteins. Analyzing the patterns, they were able to determine each protein's three-dimensional structure. Researchers at the Burnham Institute for Medical Research then combined the SSRL data with 358 protein structures determined using computer modeling techniques, creating a map of how the different proteins interact with other molecules.

"We have complete coverage for all the pathways that perform all of the organism's essential functions," said SSRL Senior Staff Scientist Ashley Deacon, core leader for the JCSG Structure Determination Core. Read more at:

7.   Herman Winick Awarded Andrei Sakharov Prize for Upholding Human Rights
       SLAC Today Article by Nicholas Bock

highlight figure
Herman Winick
Stanford Synchrotron Radiation Lightsource's Herman Winick has been awarded the Andrei Sakharov Prize, an honor given every two years by the American Physical Society in recognition of scientists who have worked to uphold human rights.

Winick, who is Assistant Director Emeritus at SSRL and Professor Emeritus in the Applied Physics and SLAC Photon Science Departments at Stanford University, will receive the prize February 14 at the American Physical Society's general meeting in Washington, D.C. He will share the award with City College of New York physicist Joseph Birman and National Science Foundation Elementary Particle Physics Program Director Moishe Pripstein.

The award is named for Andrei Sakharov, a Russian physicist and Nobel laureate who campaigned extensively against nuclear proliferation in the former Soviet Union. The prize was first given in 2006 to Cornell University physicist and Soviet exile Yuri Orlov, who, in the 1970s and 80s, was imprisoned and subsequently deported for criticizing human rights violations by the Soviet government.

"It is humbling to get a prize for which the previous winners were such incredible people, who took such serious risks and endured such serious punishments," Winick said. "Here I am in a free country, speaking my mind and trying to help these people with no thought of repercussions against me." Read more at:

8.   Submit X-ray/VUV Beam Time Requests by November 15
       (contact: C. Knotts,

X-ray/VUV Beam Time requests for the February-May 2010 scheduling period are due by November 15. Log into the User Portal to submit requests.

9.   Upcoming X-ray, VUV and Macromolecular Crystallography Proposal Deadline
       (contacts: C. Knotts,; L. Dunn,

December 1 is the next deadline for submitting new X-ray, VUV and Macromolecular Crystallography standard proposals. For more information on proposal deadlines, instructions, and forms see:

Time is reserved on many beam lines for rapid access proposals. A full listing of the Rapid Access applications is available at:

10.   Former SSRL Colleague will be Missed       

It is with sadness that we report that Peter Boyd, owner of Boyd Technologies and a former SSRL duty operator, passed away last month. Peter was a well-liked duty operator at SSRL in the 1990's who often used his excellent machining skills to help many users with sample holders and modifications. He subsequently left SSRL to start his own business machining a variety of sample holders, tools and ion chambers for synchrotron beam x-ray absorption and scattering experiments with customers at both SSRL and the ALS. We are saddened by his death and will miss him. For those of you who remember Peter, condolences can be sent to MaryBeth Boyd at Boyd Technologies, PO Box 95, Manchester, CA 95459.

11.   Please Report SSRL-Related Papers, Invited Talks, and Awards
       (contacts: C. Knotts,; L. Dunn,

It is extremely important that users not only inform us whenever work conducted at SSRL results in a publication, but also acknowledge SSRL and our funding agencies in each publication. User help is needed to keep current records on publications including refereed journal papers, conference proceedings, book chapters and theses, invited lectures and major awards and patents based at least in part on work conducted at SSRL. This information allows SSRL to demonstrate scientific achievements and productivity when responding to requests sent out by the Department of Energy and the National Institutes of Health.

This information can be submitted anytime via email message to Lisa Dunn or Cathy Knotts or via the reference submission form at:

For recent publications lists and the proper acknowledgement statements see:


SSRL Headlines is published electronically monthly to inform SSRL users, sponsors and other interested people about happenings at SSRL. SSRL is a national synchrotron user facility operated by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. Additional support for the structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH Institute for General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 30 October 2009
Content Owner: L. Dunn
Page Editor: L. Dunn