Case Center for Synchrotron Biosciences

Case Center for Synchrotron Biosciences Newsletter March 4, 2014

Facility News

"Spring" Startup

It certainly still feels like Winter if you are in New York, but the "Spring" cycle has begun as NSLS emerges from the 2 ½ month long 2013/2014 Winter shutdown. Following the successful commissioning of the NSLS-II booster ring (, NSLS operations staff were able to bring NSLS out of the Winter shutdown slightly ahead of the original schedule, with the VUV ring enjoying a 3-week period of unscheduled operations. Unfortunately, the X-ray ring has been recovering from a significant storage ring vacuum leak, but extensive conditioning with beam has allowed operations to resume on the originally scheduled date of February 19, 2014.

The final proposal request cycle for the NSLS has been completed; beamtime allocated on these proposals will be distributed over May - September 2014 rather than the standard Summer cycle. The official operations schedule for this period is currently in draft form, but is expected to contain very little shutdown time to maximize available user beamtime from now until the end of NSLS operations on September 30, 2014.

CSB Beamline Updates

Synchrotron X-ray Footprinting

During the long Winter shutdown, we have improved beamline alignment devices for X28C, creating a 100 µm pinhole for beam profiling of the beam used with the KinTek apparatus. The smaller pinhole will allow us to more accurately pinpoint the useful portion of the beam for more reliable height adjustment. We have also replaced the motorized multi-sample holder slide for smooth and reliable functioning of our work-horse steady state unit. Beamtime is in relatively high demand this cycle, so please send preferred dates and sample information as soon as possible to ensure your scheduling preferences can be met.

While we are committed to hosting a robust user program at NSLS X28C while NSLS continues to operate, we have also continued to develop the West Coast partnership at the ALS to facilitate a smooth transition of the scientific programs for the interim period until NSLS-II XFP beamline comes online. Testing of various specialized equipment that may be temporary relocated and determination of required associated control system integration needs is currently underway. An ALS site visit by CSB staff was conducted in February 2014 for coordination of logistics with ALS staff (access procedures and experimental apparatus needs). Current expectation is that both the multi-sample holder and the multi-pump/capillary flow cell system (with accessories used for live cell programs) will be relocated to ALS until XFP is available. Please contact your beamline scientist for more information about accessing the West Coast program.

NSLS-II XFP Update: CSB staff have been working closely with BNL Photon Sciences staff to move forward with development of XFP. A new project manager (Dr. Julian Adams) has come onboard at BNL to work with the NxtGen beamlines as well as Partner beamlines such as XFP. XFP has been designated as one of the first three priority beamlines in this group, with an expected completion date in late 2015 (GU beam in early 2016). A Beamline Execution Plan detailing the XFP project is in advanced draft stage; both a project review for the XFP front end and a meeting of the Beamline Advisory Team to evaluate beamline design are expected this Spring. Please see the XFP page on the CSB website for details on XFP.

X-ray Absorption Spectroscopy

Winter shutdown activities at the CSB's XAS beamlines focused on various preventative maintenance and repair activities, mostly notably reconditioning of the X3B He Displex compressor and its associated cold finger. We also installed a sagittally focusing Si(220) crystal set in the X3A monochromator. The use of Si(220) will permit XAS measurements at X3A at energies above the 14.5 keV limit achievable with Si(111), with an expected energy range of 7.4 to ~24 keV. There may be some limits on the degree of sagittal focusing that can be achieved at high energies, due to the design of the bendable second crystal. Initial evaluation has been extremely promising, and we therefore plan to keep the Si(220) crystal set in place for X3A user experiments during the Spring 2014 operations cycle.

We also continue to work with the team developing the NSLS-II Inner Shell Spectroscopy (ISS) beamline to provide optimal capabilities for biological XAS users. Our recently submitted Partner User Proposal for ISS was evaluated for feasibility by BNL Photon Sciences management, and we submitted a revised version in mid-January that took account of their feedback. Our PU Proposal underwent scientific merit review by the Spectroscopy sub-panel of the recently constituted NSLS-II Proposal Review Panel during their early February meeting, and the review results are currently under consideration by PSD management.

Macromolecular Crystallography: Scientific Highlights from Beamline X29 and Transition to NSLS-II

X29 continued its outstanding productivity during the past year, standing in second place in the world in PDB deposits, with a total of 275 PDB deposits in 2013, behind only BU17U from the SSRF in China. Several premier publications associated with beamline X29 have become available in the last quarter of 2013, including a recent publication in PNAS from from Prof. Seth Darst's group at Rockefeller University (Bae B, Davis E, Brown D, Campbell EA, Wigeshweraraj S, Darst SA. PNAS 2013 Dec 3; 110(49):19773-7). Prof. Darst's research explores the mechanism and regulation of transcription by determining 3-D structures of RNA polymerase (RNAP) and associated proteins. This publication focuses on the crystal structure of E. coli RNAP holoenzyme with or without a gene product encoded by bacteriophage T7, Gp2, to define the structure and location of the RNAP ?70 subunit inside the RNAP active site channel. The structures and associated data reveal the mechanism of inhibition of E. Coli RNAP by Gp2.

Activities also continue in the transition to NSLS-II. We submitted a Partner User Proposal (PUP) for FMX and AMX, two NIH-funded crystallography beamlines at NSLS-II, to PSD management in late September 2013. The PUP has been reviewed for feasibility by the FMX/AMX beamline scientists, and we submitted a revised version of the PUP in January 2014 based on comments received from the scientists and PSD management. The PUP recently underwent scientific merit review by the NSLS-II Proposal Review Panel (PRP) in early February 2014, and the review results are currently under consideration by PSD management.

For additional information:

Mark Chance, Director
(216) 368-4406
Jen Bohon, Beamline Scientist (X28C)
(631) 344-4613
Erik Farquhar, Beamline Scientist (X3B)
(631) 344-8174
Wuxian Shi, Beamline Scientist (X29A)
(631) 344-2099
Michael Sullivan, Chief Engineer
(631) 344-3800
John Toomey, Snr Technical Specialist
(631) 344-7057
Donald Abel, Technical Support Specialist
(631) 344-5154
Rhijuta D'Mello, Scientific Associate
(631) 344-3245

National Synchrotron Light Source
Building 725
Brookhaven National Laboratory
Upton, NY 11973