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SSRL Headlines Vol. 3, No. 9  March, 2003


Contents of This Issue:

  1. Science Highlight - Exploring the Folding Landscape of a Structured RNA by SAXS
  2. SPEAR2 Ends a Remarkable 30 Years on March 31
  3. More on SPEAR3 Installation Plans
  4. Introducing BL11-3, SSRL's Newest Beam Line
  5. Visit by Representative from U.S. Office of Management and Budget
  6. SSRLUO Update
  7. Berkeley-Stanford Summer School on Synchrotron Radiation and its Applications - June 9-13, 2003
  8. SRI 2003 8th International Conference on Synchrotron Radiation
  9. Student Tours at SSRL
  10. User Research Administration Announcements

1.  Science Highlight - Exploring the Folding Landscape of a Structured RNA by SAXS
      (contact: Ian Millett)

Determining how RNA (ribonucleic acid) folds, or "ravels", may offer a key to un-raveling how and why anomalies occur in the human genome. RNA is now known to play a pivotal role in gene silencing, gene shuffling, protein regulation and disease. However in contrast to proteins, very little is known about how RNA takes its three-dimensional shape and under certain circumstances works as an enzyme. Getting a good look at RNA in the process of folding from its initial 1-D "ribbon" state, into a 3-D "knot" (the form in which RNA is biologically functional) would be very valuable information. Enter SAXS (small angle x-ray scattering), an effective tool for time-resolved studies of structural changes which does not require crystals. A group of researchers from Stanford University have used SAXS to study the process of RNA folding in real time utilizing the SAXS synchrotron beam line at SSRL. Using SAXS, in combination with stopped-flow and continuous-flow kinetics, the researchers have directly monitored for the first time the RNA chain compaction that occurs during folding. This was done in order to determine whether compaction occurs as an early step in folding, before specific tertiary (final) structure formation, or whether it occurs as long-range contacts form. They found that RNA forms a nonspecifically collapsed intermediate shape and then searches for its final contacts within a highly structured subset of conformational space, and that RNA folding is highly path-dependent. For more information on this work and its broader implications for RNA structural biology, read the full story and cited recent publications on this work at:

2.  SPEAR2 Ends a Remarkable 30 Years on March 31
     (contact: Cathy Knotts)

This morning (March 31) at 6 am marked the end of a remarkably creative and productive period in the history of the development of synchrotron radiation science. Since the first synchrotron radiation experiments were done in 1973, SPEAR has been responsible for many innovations in source technology and new scientific methodologies. Articles in coming newsletters will highlight some of these important accomplishments. Even as the work to dismantle SPEAR2 began this morning, a small celebration was held with brief presentations being given by SLAC Director Emeritus Burton Richter and SSRL Director Keith Hodgson to highlight the history of significant research contributions from SPEAR and a vision of the bright future anticipated with the SPEAR3.

If you think things are busy at SSRL on a normal day, just hold on to your hard hats. As soon as users finished taking their last data sets at 6 am this morning, activities kicked into high gear for the SPEAR3 project installation phase as staff from engineering, mechanical systems, vacuum systems, power supply systems, instrumentation, control, protection systems, cabling, RF systems, beam line development, electrical development, mechanical engineering, electronics, operations, experimental support and many other groups began to implement a carefully coordinated installation plan. Some further details on this installation effort are found in the next highlight below.

3.  More on SPEAR3 Installation Plans
     (contact: Tom Elioff)

In order to keep the shutdown as short as possible, we have established an aggressive schedule for the installation of SPEAR3. To date, the SPEAR3 project remains on time and within budget. SPEAR2 will be removed during the month of April. Building renovations, including pouring new concrete floors in both the ring tunnel and the power supply building will be staged over the summer. Installation of new survey monuments, mounting plates, magnet girders and other technical components, shielding, cable plant and beam line front ends are scheduled from June through September. In October, the ring will be leak checked and pumped down. In the fall, we will begin commissioning the new SPEAR3 storage ring. We plan to resume user operations, at least in a commissioning mode, on many beam lines early in 2004. We will provide updates in each of the upcoming monthly newsletters and more technical information is available from the SPEAR3 web site and quarterly reports:

4.  Introducing BL11-3, SSRL's Newest Beam Line
       (contacts: Tom Rabedeau, Mike Soltis)

After extracting first light on November 25, 2002 on BL11-3, the most recent beam line to be installed on SPEAR2, optics commissioning activities began and were subsequently completed on March 5, 2003. This new beam line, utilizing a milli-radian of fan on the BL11 26-pole, 2.0-T wiggler insertion device, is a quasi-fixed energy beam line designed for shared use by the macromolecular crystallography and materials scattering communities. The beam line employs an off-cut, side scattering, focusing Si(311) crystal monochromator optimized at approximately 12,700 eV with a 200 eV tunable energy range. The accessible energy range allows for single- or multi-wavelength anomalous dispersion (SAD and MAD) experiments to be carried out at the Se edge. Vertical focusing is provided by a 1 m long Si mirror located downstream of the monochromator.

Following optics commissioning, the focus of activities at the beam line turned to the experimental instrumentation. The groundwork for this effort was laid throughout the winter as the macromolecular crystallography group worked to assemble and install the extensive hutch instrumentation and computational capabilities that are standard on all other SSRL macromolecular crystallography beam lines. Last week, the first commissioning data set from a myoglobin crystal was collected to 1.5 resolution and proved to be of very high quality. Commissioning with users continued until the end of the run and based upon the experience gained, one can be confident that BL11-3 will be up and fully operational in 2004 at the outset of the SPEAR3 era.

5.  Visit by Representative from U.S. Office of Management and Budget
       (contact: Keith Hodgson)

Joel Parriott, Budget Examiner from the Federal Office of Management and Budget (OMB), spent the day at SLAC on Monday, March 10. His visit included several hours at SSRL. He met first with a group of SSRL management and scientific staff and a range of topics, including SPEAR3 and LCLS and the science they would enable, were discussed. This was followed by a visit to several operational experiments on the floor. Included were BL11-2, a state-of-the-art XAS station dedicated to molecular environmental sciences, where Steve Conradson's group (LANL) was taking data to further their studies to obtain information valuable in aiding the remediation of radionuclides at contaminated sites like Rocky Flats. Also visited was BL11-1 for a demonstration of SSRL's high-throughput robotic crystal screening and data collection system, and a discussion with user Geoffrey Chang (Scripps) whose studies on bacterial ATP binding cassette transporters have been greatly facilitated by synchrotron diffraction studies at SSRL. Overall, the visit was very productive and Dr. Parriott seemed to gain a lot of useful information on synchrotron sources and science and the prospects for future developments.

6.  SSRLUO Update
       (contact: Uwe Bergmann, Chair, SSRLUO-EC)

SSRL's Users' Organization Executive Committee met on February 6. Much of the meeting was devoted to beam line development issues. The top priority remains to have all beam line front ends 500 mA capable when SPEAR3 turns on. Insertion device beam lines are next and bending magnet beam lines are the final priority. However, in response to a strongly expressed desire by the user community to see more beam lines up and running in early 2004, several beam line engineers have been tasked with finding ways for the bending magnet beam lines to accept currents higher than 100 mA. With this effort SSRL hopes to develop ramp-up plans that make it possible to operate many of the beam lines during much of the 2004 run while work is ongoing to eventually reach the 500 mA milestone. More details regarding beam line development plans and other topics discussed at the meeting are included in the meeting minutes at:

The next meeting will be held on Friday, May 9, 1-3 pm in SSRL Bldg. 137 3rd floor conference room. See agenda at:

7.  Berkeley-Stanford Summer School on Synchrotron Radiation and its Applications - June 9-13, 2003
       (contacts: Anders Nilsson; David Attwood)

The third Berkeley-Stanford summer school will provide basic lectures on the synchrotron radiation process, requisite technologies, and a broad range of scientific applications. Visits to both the ALS and SSRL will be included. The summer school will be limited to ~40 graduate students, with a preference for those pursuing doctoral research in the physical sciences in which synchrotron radiation is expected to play a significant role. The summer school is jointly sponsored by U.C. Berkeley, Stanford University, LBNL and SSRL. Lectures will be presented by professors and scientists from these four organizations and their user communities. The summer school will be housed at U.C. Berkeley's Clark Kerr campus. David Attwood and Anders Nilsson are co-chairing the school.

Details describing the summer school will be posted at the website ( Cost of attendance will be $625 for the one-week course (June 9-13), including lectures, shared room, breakfast and lunch. Instructions for "How to Apply" are posted to the website listed above. Applications should be submitted no later than May 1, 2003.

8.  SRI 2003 - 8th International Conference on Synchrotron Radiation

Visit for the latest information on SRI 2003. Over 650 abstracts were received by the March deadline covering a broad range of topics including new developments in synchrotron radiation sources, free-electron lasers, beam line instrumentation and experimental techniques. SRI 2003, sponsored by SSRL and the ALS, will be held August 25-29, 2003 at the Yerba Buena Center for the Arts which is centrally located in downtown San Francisco. Blocks of rooms have been reserved at nearby hotels at reduced conference rates, but attendees should make their travel arrangements early to ensure the discounted rates. Also, register for the meeting before Tuesday, June 3, 2003 to take advantage of the early registration discount.

9.  Student Tours at SSRL

In response to requests by several Stanford/SSRL faculty members, SSRL has recently played host for a number of student group tours. Dave McKay (Structural Biology/SSRL Affiliated Faculty) started off this wave of "field trips" by bringing students from his "Methods in Molecular Biophysics" class to SSRL on February 26 for a brief tour that coincided with his beam time on BL11-1. Axel Brunger (Molecular & Cellular Physiology/SSRL) coordinated a tour for a group of prospective Stanford Biophysics students on February 28. SSRL staff scientist Ashley Deacon led the tour that included a demonstration of the SSRL high-throughput crystal screening and data collection system on BL11-1. On March 6, Chris Chidsey (Chemistry/SSRL) brought a group of chemistry undergraduate students through for a tour and an XAS tutorial given by Britt Hedman (SSRL) and the user on BL7-3 (Robert Scott, Univ. of Georgia) describing his experiment. Martin Greven (Applied Physics/SSRL) and staff scientist Apurva Mehta showed students from Greven's "Intermediate Electricity and Magnetism" class around the experimental floor the afternoon of March 10.

10.  User Research Administration Announcements
       (contacts: Cathy Knotts, Lisa Dunn)

We expect that many users will want to take advantage of SPEAR3 as soon as user operations resume in early 2004, so we want to pass on a few deadlines to help users do some advance planning.

New Proposals: November 1, 2003 is the deadline for submitting new X-ray/VUV proposals. New Proposals for Macromolecular Crystallography experiments are due December 1, 2003.

Beam time requests: November 1, 2003 is also the deadline for requesting beam time on X-ray/VUV beam lines during January-April, 2004. The deadline for Macromolecular Crystallography beam time requests will be announced at a later date.

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 S ciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.

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Last Updated: 31 MAR 2003
Content Owner: L. Dunn
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