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SSRL Headlines Vol. 9, No. 5  November, 2008


Contents of this Issue:

  1. Science Highlight — Revealing a Structural Weakness of the Deadly Ebolavirus
  2. Another Successful Start-Up
  3. Beam Line 4 Update
  4. X-RAY/VUV Beam Time Requests due December 12
  5. Visitors from Shanghai
  6. SSRL Users' Organization Update
  7. Biology — Now in 3-D!
  8. ID Badges Needed to Enter SLAC National Accelerator Laboratory
  9. SLAC Linear Café Lunchtime Service Extended

1.  Science Highlight — Revealing a Structural Weakness of the Deadly Ebolavirus
       (contacts: J.E. Lee,; E.O. Saphire,

EbolaVirus figure
The crystal structure of ebolavirus GP
Scientists are one step closer to conquering the deadly Ebolavirus, thanks to research conducted at SSRL structural biology Beam Lines 9-2 and 11-1 and ALS Beam Line 5.02 by a team of researchers led by Erica Ollmann Saphire from The Scripps Research Institute. The results were published in the July 10 edition of the journal Nature.

Using macromolecular crystallography techniques, the team solved the structure of a protein on the Ebolavirus's surface, called glycoprotein GP, in complex with a rare antibody identified in a human survivor. The glycoprotein-antibody complex proved especially challenging to crystallize and subsequently, to yield well-diffracting crystals. The team grew ~50,000 crystal samples and screened 800 of the largest, using in part the highly-automated robotics hardware and software at the SSRL beam lines, before finding a sample that would diffract to 3.4 Angstroms.

The Ebolavirus causes a severe hemorrhagic fever with 50-90% lethality for which no vaccines or treatments are yet available. In order for Ebolavirus to infect a host, it must first recruit one of the host's own enzymes to uncover a portion of the glycoprotein required for infection. This work explains how GP reveals its host binding sites, drives fusion of the viral and host membranes, and disguises itself from surveillance of the immune system. The structure also explains why antibodies that neutralize the virus are so rare, identifies the very few locations on the Ebolavirus where an antibody might attach itself, and thus provides structural templates that can be used for developing vaccines and antibodies against the virus.

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

2.   Another Successful Start-up

Accelerator operations resumed for users as scheduled on November 10. Other than a minor beam loss due to a SPEAR3 RF-reflected power trip, SPEAR3 has been performing reliably with a run-time average of 99% so far. Users are getting good data and structures have been solved.

A significant step in the effort to implement top-off injection for SPEAR3 was reached during the machine studies period of November 18 when radiation measurements during top-off tests with four open beam lines confirmed that dose rates were at least a factor of four less than the best case (minimum dose) measurements made during the last user run. This dose reduction is largely, but not entirely, due to rebuild of the Booster-to-SPEAR (BTS) transport line during the recent shutdown that removed all the vacuum windows, which were previously causing an increase in injected beam size, accompanied by more beam loss and radiation dose on the floor when beam line stoppers were open. The improvement is also the result of the efforts of the accelerator physics and engineering groups, which have been engaged in the ongoing task to monitor and control the injected beam trajectory and stability. With this success, SSRL is now ready to conduct the next phase of top-off injection tests, where the normal 3-per-day beam fills will take place with stoppers open on selected beam lines over a period of many days in order to monitor long-term accumulated radiation dose. During these tests, the local area around each affected beam line will be cleared for injection. Given a successful outcome of these tests, and with the appropriate approvals, SSRL will be poised to commence routine top-off injection before the end of this user run.

Reminder: We'll be down for winter break beginning the afternoon of Friday, December 19. User Operations are planned to resume at noon, on Monday, January 5. SLAC does not accept incoming shipments during weekends or holiday breaks, and we will not be staffed to process gas orders, so please plan your data collection preparations accordingly.

3.   Beam Line 4 Update
       (contact: H. Tsuruta,

SSRL staff scientist Thomas Weiss at BL4-2. (Photo by Brad Plummer)
For the first time in more than a year, Stanford Synchrotron Radiation Lightsource users and staff now have access to a fully dedicated small angle x-ray scattering, or SAXS, beam line to study biological molecules, Beam Line 4-2. The new BL4, which was moved from a previous location on the SPEAR3 storage ring and rebuilt from the ground up, also includes two side stations, Beam Lines 4-1 and 4-3, for conducting x-ray absorption studies of biological, environmental, chemistry and materials science samples (currently in commissioning).

Commissioning of the BL4-2 end station, including new experimental instrumentation, finished last week, and the first general user group then began experiments. For more information, see the September 2008 issue of SSRL Headlines, and the beam line web page at:

4.   X-ray/VUV Beam Time Requests due December 12
       (contact: C. Knotts,

X-ray/VUV Beam Time Requests for February through May 2009 beam time are due Friday, December 12. Please use the new URA web-based interface to submit your request at:

5.   Visitors from Shanghai

Three visitors from the Shanghai Synchrotron Radiation Facility (SSRF) and the Chinese Academy of Sciences (CAS) visited SLAC last week. They included Professor Jiang Mianheng, Vice President of CAS, responsible for overseeing high tech-related research at the academy; Dr. Xu Hong-jie, Director of the Shanghai Institute of Applied Physics (SINAP), a research division of the CAS; and Mr. Sun Hui of the Bureau of Foreign Affairs at CAS. A roundtable discussion was held in the SLAC Director's office on topics of mutual interest including synchrotron radiation science and the LCLS and its science program. The group toured SSRL and LCLS, and the SIMES laboratories on the Stanford campus. The group planned to visit several other DOE National Laboratories on their trip.

6.   SSRL Users' Organization Update       
       (contacts: W. Lukens, SSRLUOEC Chair,; C.S. Kim,, Ex-Officio)

The SSRL Users' Organization Executive Committee (SSRLUOEC) met on November 25. The SSRLUOEC is working with the National Users Facility Organization (NUFO) and the Synchrotron and Neutron Users' Group (SNUG) to identify users who are interested in user advocacy. Meetings with congressional representatives to discuss the need to support basic sciences in the US are planned for February and March. If users are interested in participating in advocacy activities, please let us know.

Plans for a user survey are underway. More information will be distributed next month. Save the date - October 19-21, 2009 for the next joint SSRL/LCLS Users' Meeting and Workshops. This meeting is organized by the Vice Chairs of the respective users' organizations, Katherine Kantardjieff (SSRLUOEC Vice Chair) and Richard Lee (LCLS Vice Chair), along with SSRL and LCLS scientists. Suggestions for workshop topics are encouraged.

7.   Biology — Now in 3-D!
       November 20, 2008 SLAC Today Article by Michael Torrice

3-D Image of Steap
click on image to see large 3-d version
Physicists and astronomers are increasingly using 3-D renderings. Consider the structure of a protein solved by users at the Stanford Synchrotron Radiation Lightsource. Some proteins have deep crevices or appendages that pivot and rotate. But scientific papers by necessity present these dynamic three-dimensional structures with flat and static two-dimensional pictures. Biologists can now share 3-D images of their proteins with simple Portable Document Format files.

"So much of what we do in science is 3-D information, especially at SSRL," said SLAC National Accelerator Laboratory physicist Norman Graf. "[SSRL scientists'] whole point is to find information in 3-D."

In his own work, Graf uses PDF files to share 3-D schematics of particle detector designs. But after he read about the structure of a protein called Steap3 (, which was solved using SSRL's Beam Line 9-2, he was curious to see the protein in its true 3-D shape. Read more...

8.   ID Badges Needed to Enter SLAC National Accelerator Laboratory       

Please remember to have your photo ID out to show security when you enter the SLAC main gate. In addition, you also need to show your SLAC ID to Security in order to enter through Gate 17 or Gate 30. If you do not have your SLAC ID badge with you, security will issue a temporary ID badge (and dosimeter if appropriate) after confirming that your training is valid.

9.   SLAC Linear Café Lunchtime Service Extended       

The SLAC Linear Café has recently extended lunchtime service from 11:30 a.m. to 2:00 p.m. daily. The café will continue to remain open for snacks and beverages until 3:00 p.m. Monday through Thursday. Along with the added lunch hours, the café has updated their menu ( to include alternating hot entrées and salads in the "Good Food for You" category.


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 DEC 2008
Content Owner: L. Dunn
Page Editor: L. Dunn