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SSRL Headlines Vol. 9, No. 4  October, 2008


Contents of this Issue:

  1. Science Highlight — Role of Specific Protein Mutations in Causing Human Disease Revealed
  2. SSRL Exchanges "Laboratory" for "Lightsource" in Its Name
  3. From the SLAC Director: The Future of Photon Science at SLAC National Accelerator Laboratory
  4. LCLS/SSRL Users' Meeting Wrap-Up
  5. SSRL Users' Organization Executive Committee Update
  6. Scientific Needs for Future X-Ray Sources in the US
  7. New Safety Procedures for Hazardous, Radioactive or Nanomaterials
  8. New LHe Ordering Process for SSRL XAS Cryostats
  9. SSRL Building 120 Seismic Upgrade Project Completed Ahead of Schedule and Under Budget
  10. User Research Administration Update

1.  Science Highlight — Role of Specific Protein Mutations in Causing Human Disease Revealed
       (contact: L. Fan,; J.A. Tainer,

XPD Helicase figure
Distribution of amino acid residues corresponding to human XPD disease mutations.
Scientists are one step closer to understanding a piece of the machinery involved in DNA transcription and repair, thanks to work done in part at the SSRL macromolecular crystallography Beam Line 11-1. The team, led by The Scripps Research Institute researcher John Tainer, and colleagues worked out the structure of an important enzyme call XPD, a member of the helicase family of enzymes, found in all living organisms. The results were published in the May 2008 edition of the journal Cell.

In eukaryotes, XPD is responsible for unwinding double-stranded DNA molecules during transcription or repair. Because it plays such a key role in the DNA transcription and repair pathways, determining the structure of XPD is crucial to understanding how healthy cells operate and how defects lead to disease. Mutations in the XPD protein are associated with cancer and premature aging (progeria).

Human XPD has proved an elusive target for crystallographic studies because it is difficult to synthesize in sufficient quantities. Working with an XPD homolog from the single-celled Sulfolobus acidocaldarius, the team confirmed evidence from earlier experiments that suggested one of the four domains of the XPD structure contains an iron-sulfur containing cluster, and provided for the first time the structural basis to explain the mutations for three distinguished inherited diseases.

To learn more about this research see the full scientific highlight at:

2.  SSRL Exchanges "Laboratory" for "Lightsource" in Its Name

New SLAC logo
At a ceremony at SLAC on October 15, Dr. Patricia Dehmer, Deputy Director for Science Programs at the DOE Office of Science, announced that SLAC has been renamed to the SLAC National Accelerator Laboratory. "The new laboratory name acknowledges the distinguished accomplishments SLAC has achieved over the years, and its exciting future as a multi-program Department of Energy National Laboratory," said Under Secretary for Science Dr. Raymond L. Orbach. "The laboratory's world-leading set of core capabilities makes it a key member of the Department's National Laboratory complex, and fuels the Office of Science research capabilities for the future." As it is customary for National Laboratories to have only one "Laboratory" on site, the new SLAC name necessitated a name change also for SSRL. As a result, the Stanford Synchrotron Radiation Laboratory became the Stanford Synchrotron Radiation Lightsource. The new name maintains the SSRL abbreviation that is so well-known throughout the world-wide scientific community.

3.   From the SLAC Director: The Future of Photon Science at SLAC National Accelerator Laboratory

SLAC Director
Persis Drell
Last week I had the honor of giving the keynote address at the Linac Coherent Light Source-Stanford Synchrotron Radiation Lightsource joint annual users' meeting on the future of photon science. Since my background is in particle physics and particle astrophysics, I was a bit nervous to presume to talk to the user community about their field of expertise. However it was fun to give a talk where I could paint a picture of the future of photon science at SLAC National Accelerator Lab, motivated by the scientific goals of the field.

The future of photon science at SLAC is playing out on two very different timelines. For the postdocs and graduate students in the audience, the future is the next 3 years. And as lab director, I also have to be concerned about the future a decade from now. We have opportunities now because visionary individuals had great ideas a decade or more ago. So I also talked about the long-term future of photon science at SLAC and our strategy to deliver both world-leading capabilities to the photon science user community and innovative mission-relevant scientific discoveries for the decades to come.

The near-term future is very exciting. SPEAR3 will reach 500mA operation and new and upgraded beam lines will come into operation, adding significant new capabilities. The LCLS project will welcome its first users in 2009. The response to the first call for proposals for LCLS beam time was excellent, with 28 proposals involving 219 scientists and requests for running time that saturate the available beam time by more than a factor of two.

To talk about the longer-term photon science future at SLAC, I had to start with the scientific goals. Many of the grand challenges in the field of photon science, which can be linked directly with challenges that face our society in the areas like energy production, improved health and environmental and climate control, are focused on increasing our understanding of and ultimately controlling matter at the level of atoms, electrons and spins. The future of photon science will be defined by the tools that allow us to observe and manipulate the ultrafast timescales of electron motion, the spatial scale of atoms and the energy scale of the weak interactions that hold electrons in correlated motion with near neighbors. To fully address this science will require light sources with better spatial, temporal and energy resolution that we can currently achieve, but the sources that will deliver breakthrough progress in these areas are within our reach.

I told the user community about the potential upgrades to LCLS and a possible PEP-X program in the decade to come. I also told them how SLAC and Lawrence Berkeley National Laboratory are committed to working together to provide optimal suite of capabilities to the national light source community here on the west coast over the next decade, in a collaborative rather than competitive fashion. LBNL has potential upgrades to fully utilize their soft X-ray storage ring, the Advanced Light Source, and they have a concept design for a revolutionary soft X-ray free electron laser. Which opportunities are realized and when is not our call. But SLAC and LBNL are firmly committed to offering best suite of technical solutions possible to provide access to the most exciting science for our own research and for our users.

My final message to the users was to emphasize that even as an outsider, I am excited by the tremendous scientific opportunities in their field as the free electron laser technology opens a new frontier of basic research along with the advances in storage ring technology. In addition, it is inspiring to think that the basic research into the structure and dynamics of materials that we participate in over the next decade has the real opportunity of delivering transformational advances that will contribute to solving some of society's greatest challenges.

—Persis Drell   SLAC Today, October 24, 2008

User Mtg banner
4.   LCLS/SSRL Users' Meeting Wrap-Up
       (contact: C. Knotts,

The second joint LCLS/SSRL Users' Meeting was held October 15-18, 2008. Approximately 315 individuals participated in the various activities scheduled over the four-day event which began on Wednesday with an LCLS-themed science and development session held concurrently with two SSRL-related workshops: Advanced Topics in EXAFS Analysis and Applications; Crystallography Made Easy through Automation. Thursday was devoted to a joint LCLS/SSRL session including LCLS and SSRL overview talks, updates from Washington, the keynote speech by SLAC Director Persis Drell (as mentioned above), and science highlights. The day ended with the poster session and the Users' Meeting dinner. Activities resumed on Friday with an SSRL session devoted to science and technical developments and with two LCLS workshops: Application of Coherent X-rays at the LCLS; Atomic, Molecular & Optical Physics with the LCLS. The final event on Saturday, October 18 was an all-day joint SSRL/LCLS/ALS workshop on Soft X-ray Beam Line for Material and Energy Science at the LCLS.

As part of the meeting tradition several awards for outstanding technical and scientific achievement in synchrotron radiation-based science were presented.

The SSRL Organization Executive Committee has presented the Farrel W. Lytle award since 1998 to recognize technical or scientific achievements in synchrotron radiation research and to foster collaboration and efficient use of beam time at SSRL. This year Professor Robert A. Scott, University of Georgia received the Lytle award for his contributions to synchrotron radiation research. For the past three decades, Scott has been a leader in the use of x-ray absorption spectroscopy to study the structures of metal-containing sites inside proteins. These centers carry out the biological work of the protein. More recently, he has developed new techniques to expand the capabilities of XAS. Besides his scientific contributions, Scott has also shared his expertise in using XAS to study biological systems with many young scientists through the years. "Bob's lectures on XAS served as a model that many of us have used for our own presentations at summer schools, such as the one that SSRL now offers," said Professor James Penner-Hahn, University of Michigan.

As previously announced in the September and August editions of Headlines, respectively, the William Spicer Young Investigator Award was presented to R. Joseph Kline, a staff scientist at the National Institute of Standards and Technology (NIST) in Gaithersburg, MD (, and Ajay Virkar, a graduate student at Stanford University, received the Melvin Klein Professional Development Award (

Additionally, six graduate students received prizes for outstanding scientific poster presentations, including: Rebecca Fenn (Stanford University), Reassessing the Mechanical Properties of DNA; Sarah Hayes (University of Arizona), Characterization of Mine Tailings Using Complimentary Synchrotron Techniques; Thomas Lohmiller (UC Berkeley), What is the Role of Ca in Photosynthetic Water Oxidation: Polarized X-ray Absorption Spectroscopy of the Ca-depleted Oxygen Evolving Complex of Photosystem II; Jasquelin Pena (UC Berkeley), Zinc Surface Speciation on Biogenic Manganese (IV) Oxides: Influence of pH and Surface Coverage; Ming Yi (Stanford University), Angle-resolved Photoemission Spectroscopy on the New Iron-based High Temperature Superconductors; Diling Zhu (Stanford University), Beyond Fourier Transform Holography: Reference Guided Phase Retrieval. Read these and other abstracts at:

5.   SSRL Users' Organization Executive Committee Update       
       (contact: W. Lukens, SSRLUOEC Chair,

The SSRL Users' Organization Executive Committee (SSRLUOEC) met on October 17 immediately following the annual Users' Meeting. Newly elected representatives to the 2008-09 SSRLUOEC were announced including: Ben Gilbert, LBNL; Beth Wurzberg, Stanford University; and Brittany B. Nelson-Cheeseman, UC Berkeley. Jo Stöhr participated in this meeting to share his vision for future opportunities for x-ray science at SSRL including PEP-X. The rising cost of gases, particularly liquid helium, was discussed. Matthew Latimer and Britt Hedman discussed a plan to improve the process of ordering and charging users for liquid helium used with SSRL cryostats (see section 8. below), which was endorsed by the SSRLUOEC. The next SSRLUOEC meeting is tentatively planned in late November, and users are invited to participate to discuss any issues or suggestions they have. Information on SSRLUOEC members and activities are posted at:

6.   Scientific Needs for Future X-ray Sources in the US
       (contact: J. Stöhr,

Report Cover
At the SSRL/LCLS Users' Meeting earlier this month, I provided an update on the future of x-ray science and SSRL's strategy. As a followup to that talk, I would like to share with you a white paper that emerged from a close collaboration and many brainstorming sessions of scientists from SLAC/Stanford and LBNL/Berkeley. The SLAC and LBNL study group was co-chaired by Roger Falcone and myself and included members Uwe Bergmann, John Corlett, John Galayda, Jerry Hastings, Robert Hettel, Zahid Hussain, Janos Kirz, Bill McCurdy, Tor Raubenheimer, Fernando Sannibale, John Seeman, Z.-X. Shen, Robert Schoenlein, and Alexander Zholents. This document, which looks at the bigger picture for x-ray science in the US over the next two decades, can be viewed at
I hope you will enjoy reading it.

-Jo Stöhr

7.   New Safety Procedures for Hazardous, Radioactive or Nanomaterials

       (contact: M. Padilla,

SSRL is in the process of updating our safety and user support process for the next run, and additional instructions will be distributed shortly. In the mean time, if your proposed experiments involve hazards, please refer to the safety information which was recently updated on our website or contact Matt Padilla for further instructions. Please note that there are new requirements for radioactive experiments & experiments involving nanoparticles, see:

Hazardous & Radioactive Materials

Procedure for Using Radioactive Materials at SSRL Forms (Radioactive Materials Shipment)

30-Day and 7-day Advance Notification

1-Day Advance Notification

Sample Holder Catalog

Nanomaterials Safety Plan

NFPA Chemical Labeling System

If you have any questions, just let us know. We look forward to your visit to SSRL!

8.   New LHe Ordering Process for SSRL XAS Cryostats

A new process for ordering liquid helium (LHe) for SSRL XAS users has been implemented, removing ordering responsibility from users and replacing it with a system where users will be charged a fixed amount for LHe use per-shift of beam time. This change comes in response to a number of factors, including the rising cost of LHe, user concerns about cost and inefficiency/inequity of only being able to buy LHe in 100 liter quantities, and staff concerns about maintaining sufficient supply. Please note that this change only applies to SSRL users of SMB and MEIS XAS cryostats; other users of LHe at SSRL will still be responsible for ordering LHe themselves in the standard way, see

Under the new system, SSRL staff will maintain sufficient supply of LHe for beam lines where the users have requested and are scheduled to use an SSRL XAS cryostat - either the standard Oxford XAS cryostat or the Cryo Industries LHe cryostream typically used for single crystal XAS and low-energy XAS studies. After their beam time, the user's account will be charged a fixed per-shift amount for the number of shifts the cryostat is used. The per-shift charge will be in the $50-$80 range depending on the type of cryostat and price of LHe currently being negotiated with suppliers for the coming run. The per-shift charge is based on an assessment of average use rates for the two types of cryostats. An adjustment (surcharge or discount) will be made, however, for users that intentionally run at a much higher or lower use rate. Please inform staff ahead of your beam time if you intend to operate in a high or low use-rate mode.

The rates charged for LHe will be fixed for each scheduling period of the run, but adjustments will be made between scheduling periods if necessary. We hope that this new system will simplify the process for XAS cryostat users, make the LHe supply more dependable, and make the charge paid by users for LHe more predictable and equitable. Questions or concerns should be directed to Matthew Latimer (650-926-4944,

9.   SSRL Building 120 Seismic Upgrade Project Completed Ahead of Schedule and Under Budget
Users visiting SSRL over the last several years may have noticed some construction activities in Building 120. The need for seismic retrofit upgrades was identified from earlier studies and the construction added bracing to several walls in Building 120. We appreciated your patience as the last of the upgrades were completed this past summer. We are pleased to report that the construction project was completed two weeks ahead of schedule and under budget.

10.   User Research Administration Update
       (contact: C. Knotts,

X-ray/VUV Beam Line Schedule Posted: The schedule for the next scheduling period (~November 2008 through February 2009) has been posted.

If you find that you can not utilize your scheduled time, please inform us immediately so that we can try to reallocate that time to another user. We were significantly oversubscribed on many beam lines. If your request was not scheduled during this scheduling period and you are interested in requesting time in the next scheduling period, please submit your X-ray/VUV beam time request before the December 5 deadline.

Please refer to the SPEAR operating schedule which provides information on dates when we will be DOWN for Maintenance, Accelerator Physics or Holiday breaks so that you can plan your visits accordingly.

Most X-ray/VUV beam lines officially turn over to the next user at 3 pm depending on the equipment requirements and staff availability, but usually it much earlier than this. Someone from your group should plan to be available beginning at 8 am in case staff who are setting up for your beam time have questions.

Macromolecular Crystallography: The beam time schedule covering mid November through February 2009 for macromolecular crystallography experiments is also posted at:

New macromolecular crystallography proposals are due by December 1.


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: 03 NOV 2008
Content Owner: L. Dunn
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