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SSRL Headlines Vol. 6, No. 10  May, 2006


Contents of this Issue:

  1. Science Highlight — Revealing the Structure of a Hereditary Disease
  2. New Information in the Fight against Drug-resistant Bacteria
  3. Beam Line 7 Gets a Makeover
  4. Electrical Safety Month across the DOE Complex
  5. DOE Officials Visit SLAC
  6. Spring SLAC Policy Committee Meeting
  7. Workshop on Small-Angle X-ray Scattering and Diffraction Studies in Structural Biology
  8. SSRL Remote Access Workshop to be Held in New York
  9. Wrap-up on First Annual Workshop on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences
  10. Macromolecular Crystallography Proposals due July 1
  11. Photon Science Job Opportunities

1.  Science Highlight — Revealing the Structure of a Hereditary Disease
      (contact: C.S. Raman,

  Urine from HCP patients assumes an intense red fluorescence (left) when exposed to long-wavelength UV light and indicates the presence of coproporphyrin III. Normal urine (right) does not show this.
X-ray crystallography studies at the Stanford Synchrotron Radiation Laboratory recently shone light on a human enzyme that helps synthesize heme, the iron-containing pigment that helps carry oxygen to all parts of our bodies. There are many enzymes along the chemical pathway that produces heme. Defects in any one of the enzymes cause different types of porphyria, a set of symptoms that includes acute pain, neurological problems, and even the madness suffered by King George III.

Researchers from the University of Texas Medical School gained new insight into one of these enzymes, called coproporphyrinogen oxidase, or CPO. CPO executes one of the later steps in making heme, and when defective, is responsible for a hereditary type of porphyria that causes acute attacks of abdominal pain, hypertension, tachycardia and neurological dysfunction. Like a broken tool near the end of an assembly line, defective CPO cannot remove a chemical group that readies the proto-heme for its next step on the assembly line. An excess of substrate for the enzyme builds up in the body, causing at times life-threatening conditions. As well, not enough heme is produced. If diagnosed early, this type of porphyria can be treated with a high carbohydrate diet and the addition of heme through an I.V.

The x-ray crystal structure of human CPO revealed the enzyme's novel topology, and an unexpected molecule (citrate) bound to the enzyme's active site, where chemical reactions occur. The information has allowed the researchers to propose two models for how the CPO enzyme catalyzes the reactions leading to heme. It also shows how mutations in the enzyme cause it to fail at its vital job.

Heme belongs to a group of pigments called porphyrins that are essential to all life. Other members include chlorophyll, used by plants for photosynthesis, and cyanocobalamin, also known as vitamin B12.

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

2.   New Information in the Fight against Drug-resistant Bacteria
       (contact: G. Chang,

A side view of the bacterial protein EmrD.
Earlier this month SLAC's daily electronic newsletter, the SLAC Today, featured an SSRL user group's recently published results in the area of multidrug transporters. Geoffrey Chang's group at The Scripps Research Institute has determined the structure of bacterial protein (EmrD) that contributes to the ability of bacteria to become resistant to life-saving antibiotics. The structure was determined with x-ray data collected using Beam Line 11-1 at the Stanford Synchrotron Radiation Laboratory and 8.2.1 and 8.3.1 at the Advanced Light Source. The study was published May 5 in ScienceXpress.

3.   Beam Line 7 Gets a Makeover
      (contacts: T.; D. Van Campen,

1st light in the new 7-3 hutch.
SSRL BL7, which was one of the first hard x-ray insertion device beam lines in the world, has a long tradition of service to the macromolecular crystallography (BL7-1), materials scattering (BL7-2), and biological XAS (BL7-3) communities. Of course "a long tradition of service" is a nice way of saying the beam line is rather long in the tooth. Under the SPEAR3 beam line upgrade program approximately $7.5M of NIH NCRR and DOE BES funds were allocated for a complete makeover of BL7 from the insertion device all the way to the end stations. Thus the venerable BL7 delivered the last beam to users on the morning of August 1, 2005. Within hours of the start of the shut down on August 1, BL7 experienced a flurry of activity as crews began decommissioning and removing BL7 hardware. Before the end of August the space formerly occupied by BL7 was largely devoid of beam line hardware, hutches, etc.

Shortly thereafter a new BL7 began to emerge from the ashes of the old. In a previous summer shutdown the old eight-pole electromagnetic wiggler and front end were replaced by a modern 20-pole, 2.0-T hybrid wiggler and a 500-mA capable front end. With the decommissioning of the old beam line equipment complete it was time to upgrade the remainder of the beam line hardware. While new hutches took shape outside the SPEAR3 concrete shield wall, the portion of the beam line inside the SPEAR3 shielding received new masks, slits, and water-cooled mirror systems. Shielding was augmented for 500-mA SPEAR3 operations and full power injection. By the end of the summer down all the new beam line hardware located inside the SPEAR3 shielding enclosure was installed, aligned, and function tested. As SPEAR3 started up for the fall run, the installation and alignment of the optics contained in the beam transport hutch commenced. Yet more masks and slits, a new focusing monochromator for BL7-1, new LN-cooled monochromators for BL7-2 and BL7-3, new hutch stoppers, and even more shielding appeared in the BL7-0 transport hutch. Over the winter shutdown the new electrical power infrastructure for the beam line was connected to the grid and instrumentation and control electronics installations began in earnest.

Finally, following function checks in March and April, the LN monochromators were cooled. Shortly thereafter BL7 x-ray commissioning commenced with BL7-3 on May 3. Over the course of a few hours beam was conducted through the LN monochromator and made its appearance in the BL7-3 experimental hutch. This first light was followed by further commissioning of the BL7-3 monochromator and collimating mirror system. By May 15 attention turned to the BL7-2 optics commissioning followed by BL7-1 on May 19. By May 26 the first round of monochromator and mirror commissioning activities on all three branch lines was complete and light had been conducted into all three experimental hutches. The coming weeks will see additional optics characterization and configuration development activities followed by the first commissioning data collection runs. For the users of the old BL7 it has been a bit of a wait, but your patience will be rewarded shortly with three operational state-of-the-art experimental stations illuminated by a modern insertion device and optics.

4.  Electrical Safety Month across the DOE Complex
      (contact: I. Evans,

The month of May has been designated by the Department of Energy as Electrical Safety Month. In response, SLAC Today, in partnership with the SLAC Electrical Safety Committee, has been running a series of short articles to clarify the electrical safety program at SLAC, promote awareness of electrical hazards and to present electrical safety tips. These articles have covered a wide range of topics including the proper use of personal protective equipment (PPE), lock out tag out lock procedures, safe power strip and grounding practices, cable, electrical equipment and circuit breaker safety.

Circuit breaker warning labels.
In light of the serious electrical arc flash accident at SLAC in 2004, and another recently at Brookhaven National Laboratories, it's important to note that both accidents involved injuries which would have been significantly less severe if correct warning labels had been posted and the workers had worn the proper Personal Protective Equipment. Consequently, labels indicating the hazard rating and a list of PPE required for resetting a breaker are appearing on breaker panels all over SLAC. Only qualified workers with the permission of their supervisor and training in electric shock and arc flash hazards are allowed to reset breakers.

Also of particular interest to staff and users - a new Electrical Equipment Inspection Program (EEIP) has been implemented at SLAC to ensure that custom or modified electrical equipment does not shock, burn or catch fire when used properly. All electrical equipment not tested and/or inspected by a nationally recognized testing laboratory (NRTL) like Underwriters Laboratory (UL) must be inspected on-site prior to use.

For more details on these electrical safety articles see:,

5.  DOE Officials Visit SLAC

Clay Sell (third from left) at the Overlook with Keith Hodgson, Nancy Sanchez, John Galayda, Jonathan Dorfan, and Jeff Logan.
David Thomassen, Acting Associate Director of the Office of Biological & Environmental Research (BER), visited SLAC on Tuesday, May 2, and was given a tour of SSRL's experimental floor. As the Acting Associate Director, David oversees research activities including the Genomics: GTL program, low dose radiation research, climate change research, environmental remediation research, medical sciences research and user facilities for genomics, including high throughput DNA sequencing, environmental molecular science, climate change and structural biology.

On Monday, May 15, SLAC hosted Clay Sell, Deputy Secretary of Energy, for discussions with senior management, researchers and members from the Stanford Site Office as he toured the facilities. For more on his visit see:

6.   Spring SLAC Policy Committee Meeting
       (contact: K.O. Hodgson,

The meeting of the SLAC Policy Committee in early May focused on intermediate and long range strategic planning for both the Photon Science and Particle and Particle Astrophysics components of the laboratory. A perspective was provided by Jonathan Dorfan, followed by more detailed plans from Keith Hodgson and Persis Drell. The Committee heard a report of the National Academy EPP2010 decadal study from the committee chair, Harold Shapiro. SLAC's plans in the PPA area align well with the recommendations of the Committee. The SPC also heard an interim report from the chairperson of the National Academy AMO2010 decadal study and here LCLS science will align with priorities in the report. The SPC had an in-depth discussion of the faculty development plan for Photon Science that has been constituted to reflect strong growth in coming years due to the investments in SPEAR3 and LCLS and the strengthening of centers of scientific excellence. The ES&H Advisory Committee (ESHAC) reported out formally to the SPC on several areas it had investigated, among them being the user safety program at SSRL. The found the program to be very effective.

7.   Workshop on Small-Angle X-ray Scattering and Diffraction Studies in Structural Biology
       (organizers: Hiro Tsuruta,; Thomas Weiss,; Marc Niebuhr,

SSRL's SMB Bio-SAXS/D team will hold an on-site workshop on Small-Angle X-ray Scattering and Diffraction Studies in Structural Biology on July 28-31, 2006. This 4-day workshop will focus on the experimental aspects of non-crystalline diffraction techniques in biology which complement high resolution structural studies by crystallography, NMR and cryo-EM. The workshop will provide hands-on training on experimental techniques and software tutorial sessions primarily for solution x-ray scattering studies. Several shifts of beam time have been allocated for short periods of data collection by workshop participants. The latest advances in x-ray scattering and diffraction studies on biological systems will be described by several experts in a diverse spectrum of structural biology benefiting from non-crystalline diffraction studies. Also planned are presentations on complementary experimental approaches and modeling techniques. Participants will receive updates on current and future developments at SSRL BL4-2, the dedicated small angle scattering/diffraction facility for structural biology, funded by NIH NCRR and DOE BER.

8.   SSRL Remote Access Workshop to be Held in New York
       (organizers: Aina Cohen,; Clyde Smith,; Edward Snell,

Complete macromolecular crystallography experiments are now routinely being carried out at SSRL from remote locations, anywhere in the world, using secure protocols. To showcase this unique capability the SSRL SMB Macromolecular Crystallography group is taking its Remote Access Workshop on the road. This workshop will be held at the Hauptman-Woodward Medical Research Institute in Buffalo, NY on August 4. Organizers Aina Cohen and Clyde Smith (SSRL), and Edward Snell (HWI) are planning an agenda that will start with lectures and a live demonstration of remote access data collection in the morning followed by two hands-on training sessions in the afternoon. Attendees will learn about the beam line and software developments and how to successfully complete all stages of a remote access experiment. The workshop is intended to be highly practical with topics covered including:

For more information and to register see:

9.   Wrap-up on First Annual Workshop on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences
       (organizers: J. Bargar,; M. Toney,

The first annual Workshop on Synchrotron X-ray Scattering Techniques in Materials and Environmental Sciences was held at SSRL on May 16 and 17, 2006. The aim of this workshop was to provide practical knowledge in x-ray scattering methods with an emphasis on information that cannot be found in text books. More than 60 researchers, mostly graduate students and postdocs, attended the workshop. The first day consisted of introductory lectures on x-ray diffraction, how to get the most data out of your beam time, and how to apply various techniques. The second day involved "on-the-experiment" training at four of SSRL's beam lines (1-4, 2-1, 11-3, and 10-2), with those attending (the sessions were oversubscribed) gaining valuable experience from these demonstrations for future beam time on their own proposals.

Based on the comments received, the workshop was tremendously successful with one student remarking "this is the best workshop I have ever attended", and the attendees came away with new knowledge about how to efficiently collect data at SSRL's scattering beam lines. Copies of all the talks have been posted at:

We are presently deciding on the topics for next year's Synchrotron X-ray Scattering Workshop and would appreciate comments from the user community.

Workshop attendees.

10.   Macromolecular Crystallography Proposals due July 1
      (contact: L. Dunn,

July 1, 2006 is the next deadline for submitting macromolecular crystallography proposals. SSRL's current experimental run ends at 6 a.m. on Monday, August 7. Proposals submitted in July will be eligible for beam time when SSRL user operations resume in early November 2006. For more information see Proposal Submittal and Scheduling Procedures for Macromolecular Beam Lines at SSRL.

11.   Photon Science Job Opportunities

A number of positions are currently available at the LCLS, LUSI and SSRL. Please refer to the Photon Science Job Openings page for more information about these job opportunities.


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: 31 MAY 2006
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