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Update on Biological Small Angle X-ray Scattering (non-crystalline diffraction) program and outcome of the NCRR/BER review. SMB SAC meeting March 28, 2010. SSRL. Hiro T suruta. Hiro Tsuruta (Sr Sci) Thomas Weiss (Staff Sci) Associate staff scientist (vacant since early February, 2010)

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Update on Biological Small Angle X-ray Scattering (non-crystalline diffraction) program and outcome of the NCRR/BER review

SMB SAC meeting

March 28, 2010


Hiro Tsuruta

current smb saxs d personnel
Hiro Tsuruta (Sr Sci)

Thomas Weiss (Staff Sci)

Associate staff scientist (vacant since early February, 2010)

Ping Liu (Sci. Prgr)

Lester Carter (PD)

Shared resource for mechanical and electronics developments

Thomas Eriksson (MC) manages the linux PC cluster on BL 4-2.

Support personnel proposed in the BER funding component…

Current SMB SAXS/D personnel
  • Wrapping up hiring process to fill the assoc. sci. slot.
  • Onboard in May-June expected.
update funding opportunities
ARRA project funded

Supplements the core NIH NCRR grant

1. Drug target screening for prion deseases (Prusiner, Schoichet, UCSF)

studying promiscuous colloids

high throughput screening for agents modifying PrPC assembly

2. Helps accelerate software developments for HT solution scattering

On-going discussion on collaboration with the Prusiner group

Schoichet very interested

Initiating collaboration with the Mochly-Rosen group (Med School) on PKC

Other targets in discussion (HIV protease, virus capsid assembly)

Dr. Lester Carter joined in January as postdoctoral associate.

Wyatt DLS plate reader delivered in January (characterization experiments)

Update: funding opportunities
  • Solution scattering collaborations in PSI Phase III projects
  • High Throughput Structure Determination Centers (U57)
    • Joint Center for Structural Genomics (I. Wilson, Scripps)
    • New York SGX Research Center (S. Almo, Einstein College of Med.)
  • Consortia for HT Enabled Structural Biology Partnerships (U01)
    • Caulobacter crescentus structural genomics (H. McAdams)
    • Protein-Specific Crystallization - a Biology Driver (G. DeTitta, HWI)
    • National Center for Dynamic Interactome Research (M. Rout, Rockefeller)
update recent achievements in technological developments
High throughput solution scattering developments

“Autosampler” version 1.5 in regular use

3 min per a sample/buffer measurement (10 3s exposures + cell cleaning)

<2% failure in sample loading

UV/vis spectrophotomer for in-situ concentration measurements

SolSAXS tab in Blu-Ice

Continuous upgrades of SasTool for real time data processing (WindowsPC + linux)

AbsTool for UV/vis spec data processing

Version 2.0 in assembly

kap95 (NPC), Sali et al.

Recorded with Autosampler

August 2009

Syringe needle

0.50 mg/ml

0.25 mg/ml


0.125 mg/ml

0.125 mg/mL

1.7m distance

Update: recent achievements in technological developments

Improved beam stability (~10mm level)

  • Mirror pitch feedback system
  • Improved small angle resolution
  • Improved data accuracy (0.1-0.2Å in Rg)
  • Lower protein concentration (~0.2-0.3g/l)
  • Synergic use of Rayonix MX225HE

Time-resolved studies

  • Integration of ADC board/counter
  • TRSAXS tab in Blu-Ice
  • Next step: Pilatus 300K control in Blu-Ice

Ver. 1.4

recent achievements cont
Evaluated lipid support (polymer)
  • 1s exposure sufficient

LCP sample holder, BL4-2


LCP sandwich plate


Recent achievements (cont.)

High throught lipid phase diagram measurements

  • Membrane protein crytals tend to form near phase boundaries.
  • Effects of precipitates/protein on lipid phase diagram
  • Screening of newly synthesized lipids
  • Lipid Cubic Phase sandwich plates from Vadim Cherezov, JCIMPT Scripps
  • Lipid sample positions recorded by a crystal imager at Scripps.
  • LipSAXS tab in Blu-Ice reads in sample positions, aligns and measures each of 96 samples automatically.
  • Currently ~2h per plate. ~2-3 shifts every month.
  • Improving alignment accuracy (clearer fiducial markers)
  • Automated peak fit software in development (T. Weiss)
update on user program in smb saxs on bl4 2
Update on User Program in SMB SAXS on Bl4-2

User demography FY09 - FY10-1

Midwest 2%












Bay Area



Average length beam time FY09 & 10-1

FY10-1 average:

1.6 day [can’t do more]












Proposals and users:

  • 40-50 active proposals at a given time
  • ~10 new regular proposals received each deadline
  • New users and returning experienced users
  • Macromolecular crystallography users constitute

50% of all spokespersons (FY09)

  • Reaching out beyond CA & Western states

Beam time: requested vs scheduled

  • Max request/available = 1.55 [1.41 FY10-3]
  • Min request/available = 1.17 [1.08 FY10-3]

(FY09 &10#1, excluding Rapid Access)

  • High throughput development shortens required beam time.
  • Solution scattering block scheduling whenever possible (1.7m distance, MX225HE, Autosampler, 0.007
  • Rapid access brings new users.
  • Remote access trial successful.
  • Cutting down Facility time in FY10-3
  • Are we hurting ourselves by own success in
  • accommodating multiple techniques?
  • - Technological developments vs running user program. Clearly busy with the latter.
  • How to schedule BT shorter than 3 shifts without staffing increase?
  • Do we want to offer remote access?
development priorities in nih ber grant
Development priorities in NIH/BER grant
  • High throughput solution x-ray scattering studies
    • Refine existing system (2010 thru early 2011)
    • Droplet geometry (late 2010 thru 2011)
    • Software development for data quality evaluation (2010 thru 2011)
    • Software development for passing fully processed data to IMP etc (late 2010 thru 2011)
    • Microfluidic sample handling (2011-2014)
    • Structural model evaluation software (2011-2012)
    • New computational method(s) for structure modeling
  • Time-resolved technologies
    • Stopped-flow upgrade, replacing an old one with a BioLogic SF (2010-2011)
    • Pilatus detector upgrade to Pilatus 400k (4 independent triggers) (2012)
    • Nd-YAG laser upgrade (2012)
    • Raman converter for T-jump (2012)
    • Microfluidic continuous-flow (turbulent) mixer (2013)
  • Microfocus SAXS/D (as currently proposed, alternate approach discussed later)
    • Microfocus optics (originally proposed XRadia system no longer available)
    • Associated hardware upgrades
    • Hutch extension

- Some of the proposed developments are extension/enhancement or carried-over of the developments in the last grant period.

- Personnel resource limits developments, especially because of strong user program.

nih grant review panel critiques on smb saxs and response
NIH grant review panel critiques on SMB SAXS and response
  • Panel encourages interaction with LCLS.
    • XPCS is an area of potential interest, but few applications in biology currently envisioned.
  • Some resource transfer from MC to SAXS
    • Related shift/new developments at ESRF and ALS/LBL.
    • SMB SAC inputs needed.
  • Suggested opportunities for data processing/analysis software in solution SAXS
    • Strongly agreed. Getting started on data evaluation software development (ARRA PD).
    • Currently resource limited. Envision some shift of bioSAXS programming resource from Blu-Ice developments. Additional programming resource desired.
    • Envision collaboration with external groups, e.g. A. Sali (UCSF)
    • Potential collaboration with the cryoEM community, e.g. W. Chiu (Baylor)
  • Convert a MC station to a HT SAXS station
    • Not an effective approach for many reasons.
    • HT developments help create solution scattering beam time. [need support personnel]
    • SSRL plans on building an in-vacuum undulator SAXS station (mostly non-bio studies).
    • Possible micro-focus opportunities there if built.
    • Willing to take an active role in its planning and development.
  • Inter-subgroup collaboration (more horizontally integrated management)
    • SMB SAXS has benefitted for years, e.g. Blu-Ice.
    • Pilatus integration and shutter-less data collection with MC.
    • Stopped-flow and microfluidic (rapid freezing) with XAS.
micro focus saxs for structural biology in nih ncrr grant 2010 2014
Micro-focus SAXS for structural biology in NIH-NCRR grant (2010-2014)
  • Micro-focus optics and associated upgrades on BL4-2
    • Virtual source upstream within BL 4-2 hutch
    • A KB mirror system (XRadia) for ~5:1 demagnification
    • Ray-tracing indicates unapertured beam size 50mmx100mm (FWHM).
    • 1013 or 5x1012 ph/s in 50x50 or 25x25 mm2 (multilayer mono @ 500mA)
    • 10x10 mm2 possible at expense of flux
    • BL4-2 hutch extension and hutch table improvement would be requested to BER.
    • Full funding anticipated, but XRadia discontinued KB mirror systems.
  • Alternate strategy of mutual benefits
    • Develop a microfocus capability on an undulator station (upstream hutch)
    • Shared optics with the downstream SAXS/WAXS station for mat’l studies
    • Time-share
  • Benefits to SSRL
    • Help develop the in-vacuum undulator SAXS/WAXS station
    • Potential for non-bio microfocus SAXS studies
    • Maintain all of existing capabilities on 4-2 (high demand, frequent turn-around, multiple-mode of experiments for solution, lipid, fiber studies)

SMB SAC discussion needed on these future developments.