Case Center for Synchrotron Biosciences

Case Center for Synchrotron Biosciences Newsletter Dec. 1, 2014

CSB NIH Funding Renewed

In August 2014, we received notification from the NIH that our 5 year P30 Center renewal proposal was funded for the September 2014 - August 2019 period. This grant will support transition of our user-focused scientific program from NSLS to NSLS-II, including the outstanding user support that you have grown used to over many years at NSLS.

Facility News

Last Light, First Light

The NSLS X-ray and VUV shutters closed for the last time as scheduled at 4:00PM on Tuesday September 30, 2014. The "Last Light" celebration, attended by more than 500 past and present users and support staff, commemorated the conclusion of NSLS operations.

Less than one month later, at 10:32AM on October 23, 2014, the NSLS-II opened x-ray shutters for the first time, achieving "First Light" at the CSX beamline. Since then, several other project beamlines have also taken this step. The NSLS-II Project also recently received approval for the start of routine operations at the facility, and has accepted user proposals on the CSX beamline for the Spring cycle.

Construction activities continue at a frenzied pace at NSLS-II, with a number of new beamlines entering the construction phase while the NSLS-II project beamlines are either commissioning or nearing the final stages of beamline installation.

CSB Beamline Updates

Synchrotron X-ray Footprinting: Transition to NSLS-II XFP

Transition update: We are now in the transition period between NSLS and NSLS-II, and the footprinting program at the Advanced Light Source (ALS) at Lawrence Berkeley National Laboratory (Berkeley, CA) is up and running. A lively workshop was held at the ALS Users. Meeting in October to showcase the new capabilities available at this location (summary below). The CSB endstation at the ALS will support both the multi-sample holder and the multi-pump/capillary flow cell system (with accessories used for live cell programs), but does not support the KinTek. Capillary flow experiments (minimum volume of 100 µL) are recommended when possible for the beamline configurations available.

Beamtime at ALS 3.2.1 (similar to unfocused X28C) can be obtained generally within 2 weeks of request, and is suitable for smaller proteins in simple buffers. Beamtime at 5.3.1 is constrained, available approximately 4-6 days every 2 months, with the first beamtime scheduled from November 20-25. This is a focused beamline providing approximately 30-fold increase in flux density compared to NSLS X28C, and is appropriate for complex protein preparations and in vivo studies. The end-station will support a polymicro-capillary flow system for sample volumes of 100 to 200 µL / time point (currently working on pushing this down to 50 µL minimum). Irradiation time can be varied from 0.1 to 0.8 milliseconds. Please consider sending additional sample for DR tests prior to the actual sample irradiation. This test can be done at 3.2.1 with just 10 µl / irradiation before or after the scheduled run at 5.3.1.

Beamtime for 5.3.1 will be announced approximately 2-3 weeks prior to availability and is not flexible, so please contact Sayan Gupta ( or Wuxian Shi ( as soon as you know you will require beamtime on this line for your project to be assisted with scheduling. The earlier that you get your request in, the more likely that your project can be accommodated in the next run, so please let us know what you need!

ALS XFP Workshop Summary: A workshop entitled "X-Ray Footprinting at the ALS: New Opportunities in Structural Biology" at the ALS Users Meeting on October 8, 2014 brought together a lively and engaged group of researchers from around the country to discuss the capabilities of footprinting, as well as recent exciting XFP results. The morning session covered experimental techniques, starting off with Corie Ralston (LBNL), Janna Kiselar, Sichun Yang and Parminder Kaur (Case Western Reserve University) who provided tutorials on technique fundamentals, data analysis and new software available for the technique, as well as hybrid approaches (SAXS and XFP). The afternoon session covered recent science highlights, including exciting results on ribosome assembly in live cells by Sarah Woodson (Johns Hopkins University), the conformational changes governing photoprotection in cyanobacteria by Cheryl Kerfeld (Michigan State University), analysis of amyloid fibrils by Janna Kiselar (Case Western Reserve University), internal water interactions in membrane proteins by Sayan Gupta (LBNL), determining antibody conformations by Galahad Deperalta (Genentech), and HIV ENV glycoprotein activation by Mike Guttman (University of Washington). The workshop concluded with a talk by Jen Bohon (Case Western Reserve University and BNL) describing the capabilities of the new XFP beamline currently under construction at the NSLS NSLS-II, and a tour of the ALS beamlines now supporting the XFP community.

NSLS-II XFP Update: The XFP beamline project, now formally part of the "Partner" beamline portfolio at NSLS-II, is moving forward in step with the first set of NxtGen beamlines at NSLS-II, with an expected completion date in early 2016. The XFP project welcomes Dr. Andrew Broadbent as the new Portfolio Manager for Partner beamlines at NSLS-II, who will be helping to chaperone the project through the construction process. Endstation equipment and beamline components are rapidly being packaged and moved from NSLS X28C to NSLS-II, and a new construction cage is expected to be erected on the floor at 17-BM (XFP sector) by the end of the month. A formal preliminary design review for the beamline is expected to occur in January 2015. For details on the design and to follow the latest progress on the project, please see the XFP page on the CSB website.

XAS User Support at the Stanford Synchrotron Radiation Lightsource

BNL Photon Sciences and the Stanford Synchrotron Radiation Lightsource recently finalized an agreement to operate SSRL beamline 2-2, with 80% of the beamtime reserved for NSLS XAS users. For full details of the SSRL 2-2 transition program, including proposal submission procedures and beamline capabilities, see the Hard X-ray Spectroscopy at SSRL page on the NSLS-II Transition website.

The CSB is a partner in this effort, and 25% of available NSLS time on SSRL 2-2 is reserved specifically for proposals from the biological XAS community that we supported at NSLS X3A and X3B (approximately 2 months in each 9 month run year). During SSRL 2-2 beamtime scheduled for biological users, Erik Farquhar will be onsite providing user support. We recently shipped the Displex cryostat and 13 element Ge fluorescence detector from beamline X3A to SSRL for installation into the endstation. Note that SSRL 2-2 is an unfocused beamline on an SSRL bending magnet source, so it has somewhat lower flux than the SSRL wiggler beamlines. Considering the flux and detector capabilities, SSRL 2-2 will likely be best suited for studies of model complexes and more concentrated radiation sensitive metalloproteins.

Importantly, all proposals and requests for SSRL 2-2 beamtime will be submitted via the new NSLS-II PASS system. The deadline for beamtime requests for the February-May 2015 scheduling period is a month away, on Friday, December 19, 2014. Feel free to contact Erik Farquhar or Klaus Attenkofer with questions about the SSRL XAS Transition program.

Macromolecular Crystallography: Transition to NSLS-II

As most of you may know already, CSB is an approved Partner User team at the two new crystallography beamlines, FMX and AMX, at NSLS-II. FMX is a micro-focusing beamline with beam sizes of 1-20 microns. The flux will be in the range of 1013 photon/s, with a broad energy range of is 5-30 keV. AMX is a mini- focusing beamline with beam size of 10-100 microns and similar flux of 1013 photon/s. Both beamlines will be highly automated with advanced robotics to handle crystals and will also support in situ crystal screening and data collection in crystallization plates. The estimated starting date for FMX and AMX operation is mid-2016.

A First Experiments Science workshop for ABBIX beamlines (FMX/AMX and LIX, an X-ray scattering beamline) is being organized by Photon Sciences at BNL in late January 2015. The workshop will focus on applications of the advanced capabilities of the new beamlines, particularly the micro beam ability at FMX and automation in beamline control, data collection, data processing and structural solving at both FMX and AMX. The workshop is a preparatory step for the submission of First Experiment proposals for ABBIX beamlines which will be due in mid-to-late 2015.

During this transition time, all MX users are encouraged to apply for beamtime at other synchrotron facilities, including APS, MacCHESS and SSRL. In addition, see NSLS-II.s MX Transition page for information on access to the bending magnet beamline 14-1 at SSRL for MX experiments.

I hope to see you all at the ABBIX First Experiments Workshop and encourage you to submit First Experiment proposals next year.

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

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