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SSRL Headlines Vol. 4, No. 8  February, 2004


Contents of this Issue:

  1. Science Highlight — LCLS -Faster X-ray Pulses with Foil
  2. Translation of the DNA Code into Proteins by RNA Polymerase - Revelations in the Working of a Molecular Machine
  3. SPEAR3 Commissioning Update
  4. Stanford-Berkeley Physical Sciences Summer School July 25-30, 2004
  5. Reserve a Room at the SLAC Guest House for Your Next Trip to SSRL to Use SPEAR3
  6. Acknowledge, Acknowledge, Acknowledge
  7. User Administration Update

1.  Science Highlight - LCLS -Faster X-ray Pulses with Foil
      (contact: Paul Emma)

Computer simulations have shown that by using a cleverly placed piece of slotted foil, the Linac Coherent Light Source (LCLS) will be able to produce brilliant x-ray pulses that are extremely short, a few femtoseconds (a femtosecond is a quadrillionth of a second), in duration. This pulse length, which is a factor of more than 200 times shorter than the LCLS baseline design, will dramatically increase LCLS' x-ray time resolution, giving scientists the ability to study the movement of matter at atomic scales and accessing the structural changes occurring in the making or breaking of chemical bonds. The key to short x-rays pulses is compressing the electron bunches that create them. In the LCLS, bunches will be shortened with bunch compressors, 3-sided detours in the linac created by 4 magnets that pull the electrons temporarily off course. The slotted foil will take advantage of the bunch orientation within the compressor to perturb 99% of the electrons and produce an effective bunch as short as a few femtoseconds in duration.

As electron bunches proceed down the linac, for LCLS they will be accelerated with 14.3 billion electron volts of energy by radio frequency (RF) waves. Using a special mode of acceleration, the tail of the electron bunch can be given a higher energy than the head (technically referred to as a chirped beam). When the higher-energy electrons at the end of the bunch take a shorter route around the bends through the compressor magnets, they catch up to the front, in effect making the bunch shorter. The slotted foil will be placed at the crest of the bunch compressor's bend, where the electrons are spread out perpendicular to their trajectory (and there is a correlation between space and time). A mere 100 million electrons in the center of the bunch will successfully pass through the 250 micron (one millionth of a meter) slit in the foil unaltered; the other 6 billion electrons will penetrate the foil and are subsequently scattered in such a manner that they are not amplified by the laser amplification process. It is this selective amplification that yields a few femtosecond slice of electrons, which then create the ultra-short x-ray pulse when they are passed through the long LCLS undulator.

For more information on this work see:

2.  Translation of the DNA Code into Proteins by RNA Polymerase - Revelations in the Working of a Molecular Machine
       (contact: Roger Kornberg)

Professor Roger D. Kornberg and his group in the Stanford University School of Medicine have devoted more than 20 years to the study of the process by which genetic information encoded in all living things by DNA is processed into a message (a process called transcription that produces messenger RNA) that then directs the synthesis of proteins. A breakthrough paper detailing the structures of the core RNA Polymerase II protein was published in Science in April 2000 and followed by two more papers in Science a year later. The studies published in 2001 made use of synchrotron data from SSRL to reveal the molecular structure at a resolution of 2.7 and a lower resolution structure of the enzyme in the process of transcribing a fragment of DNA into RNA [1]. This pioneering work has continued and another pair of seminal papers has just appeared in Science [2,3]. A highlight summarizing the work in the same issue of Science states that "Initiation of transcription in eukaryotes involves the assembly of a large complex, composed of RNA polymerase II (pol II) and five general transcription factors, at the gene promoter. The transcription factor TFIIB plays a role in bridging between promoter DNA and pol II. Bushnell et al. (p. 983) have determined the structure of a complex of the 10-subunit yeast RNA pol II with TFIIB at 4.5 resolution. Using structural information available on the other four transcription factors, TFIID, TFIIE, TFIIF, and TFIIH, they propose a nearly complete model of the transcription initiation complex. Westover et al. (p. 1014) provide new insights into transcription itself, through the 3.6 structure of pol II in a complex with synthetic DNA and RNA oligonucleotides. The structure reveals how the RNA transcript is separated from the DNA template during transcription."

The development [4] and more recent full deployment of an automated robotic screening system at SSRL, enabled by funding provided by the National Institutes of Health, made the job of finding good diffracting crystals for these studies much faster and more efficient. This automated system uses tiny frozen crystals stored on nylon loops at the end of metal pins. A robotic arm retrieves each pin and aligns the crystal in the path of the x-ray beam. The robot can automatically test 288 samples without the need for researchers to manually transfer each sample as was done in the past. "It saves a lot of time while optimizing the quality of the data," said SSRL scientist Mike Soltis, head of the macromolecular crystallography group. "With the new system, the Kornberg group screened 130 crystals in seven hours without losing any. Two weeks earlier, they had manually mounted 100 crystals in 24 hours, losing a few crystals and much sleep in the process. The new automated screening system significantly reduces the time to complete studies of the complexity of RNA polymerase." This new automated robotic screening system will be available to all of SSRL's general users doing macromolecular crystallography as they come back in the new era of SPEAR3 operations.

  1. See polymerase.html
  2. D. A. Bushnell et al. Science 303, 983 (2004)
  3. K. D. Westover et al. Science 303, 1014 (2004)
  4. A. E. Cohen et al. J. Appl. Cryst. 35, 720 (2002).

3.  SPEAR3 Commissioning Update
       (contact: James Safranek)

SPEAR3 commissioning continues to proceed remarkably smoothly, thanks to the efforts of the SSRL staff and visitors from laboratories world-wide. 100 mA was first stored on January 22, a remarkably short time since first injection in mid December. Since then, the lifetime has been steadily increasing with vacuum scrubbing, reaching 13 hours (and climbing) at 100 mA prior to the week-long shutdown starting February 23. Measurements of the electron orbit show that it is extremely stable. For example, the fill-to-fill reproducibility of the orbit at the beam positions monitors (BPMs) is about 1 micron. Without feedback, the orbit drifts only a few tens of microns over the course of many hours. With orbit feedback, this is reduced to about 1 micron, as measured by the BPMs. The rms orbit motion in frequencies between 1 and 100 Hz is about 2 microns, which compares well to other 3rd generation light sources. Later this year, we will be implementing a fast orbit feedback to further damp these frequencies. The linear optics functions have been corrected to within a couple percent of design. Measurements of the nonlinear optics distortions are also quite close to predictions, which has resulted in good injection efficiency and lifetime (for this stage of vacuum conditioning).The remaining days of storage ring commissioning will be dedicated to investigating how much we can push the optics to allow smaller gaps in future IDs, commissioning the LIONs (a beam containment system), and preparing to deliver beam to beam lines in early March. The speed and relative ease of commissioning is a testimony to the excellent design, engineering, and construction work done by the SSRL and SLAC staff. For more information on SPEAR3 see:

4.  Stanford-Berkeley Physical Sciences Summer School July 25-30, 2004
       (contacts: Anders Nilsson; David Attwod)

The fourth Stanford-Berkeley school on synchrotron radiation and its applications, co-chaired by Anders Nilsson and David Attwood, will provide basic lectures on the synchrotron radiation process, requisite technologies, and a broad range of scientific applications. Visits to both SSRL and the ALS in Berkeley will be included, with opportunities to interact with the professional staff and graduate students at both facilities. The summer school will be held at Stanford University. Full information on planned lectures, housing arrangements and costs will follow. The deadline for applications is May 1, 2004.

5.  Reserve a Room at the SLAC Guest House for Your Next Trip to SSRL to Use SPEAR3
       (contact: Cathy Knotts)

SPEAR3 is running! When user operations resume in March 2004, users are encouraged to take advantage of the new on-site SLAC Guest House, which opened in June 2003. The Guest House is very conveniently located relative to the SSRL storage ring (a few minutes walk) and provides users with comfortable, convenient accommodations at reasonable rates; cable TV and DVD; high-speed, in-room internet access; complimentary coffee/tea; free parking; free fitness center; laundry facilities; and a 24-hour gift shop. The Guest House offers standard rooms with full size bed ($50), larger rooms with queen size bed ($65), and shared rooms with bunk beds ($32.50); all rooms have a private bathroom. For more information or to make reservations, go on-line to:

6.  Acknowledge, Acknowledge, Acknowledge
       (contact: Keith Hodgson)

It is extremely important that users not only inform us whenever work conducted at SSRL results in a publication, but also to acknowledge SSRL and our funding agencies in each publication. User help is needed to keep up-to-date listings for all peer-reviewed journal papers, book chapters, conference proceedings and theses based at least in part on work conducted at SSRL. These publication lists allow SSRL to demonstrate scientific achievements and productivity. Many thanks to SSRL spokespersons who responded to our recent request for pubs, patents and awards. We will have many more opportunities to report on publications so if you did not get the chance to respond to that request, please take a few minutes to review our publications and theses lists and let us know if there are other papers that should be included. For publications lists and the proper acknowledgement statements see

7.  User Administration Update
       (contacts: Cathy Knotts; Lisa Dunn)

User operations with SPEAR3 resume on many beam lines in March, paced by beam line re-commissioning and startup with the new machine. Updated information on beam line availability can be found at: The X-ray/VUV schedule for the first scheduling period has been distributed. X-ray/VUV beam time requests for the second scheduling period (mid May-early August) are due on March 5, 2004. Macromolecular crystallography beam time requests for the next scheduling period are due on April 17, 2004.

Macromolecular crystallography (MC) proposals are due April 1, 2004. Proposals submitted by April 1 will be eligible for beam time beginning in June 2004. Proposals should be submitted electronically to Lisa Dunn ( In addition, rapid access proposals for hot new MC projects can be submitted at any time. Rapid access proposals are reviewed for scientific merit and may be eligible for several shifts reserved monthly for this purpose. Information on crystallography proposals can be found at:


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: 27 FEB 2004
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