Collecting Macromolecular Crystallographic Data at Synchrotrons Andrew Howard
- Slides: 24
Collecting Macromolecular Crystallographic Data at Synchrotrons Andrew Howard ACA Summer School, 12 July 2007 Updated slightly November 2018
Synchrotrons are useful, not just fashionable • You can do almost any experiment better and faster at a storage ring than in a conventional lab; and there are experiments that you can only do at a storage ring.
What we need to think about • Why synchrotrons help: Factors, parameters • How they make things harder • How synchrotron data collection is different from domestic data collection • How macromolecular crystallography is different from other storage-ring apps
How synchrotrons help • Fluence • 1013 Xph/s/mm 2 • Brilliance • 1017 Xph/s/mm 2/mrad 2 • Tunability • E = 12398. 0 ± 0. 4 e. V • Collimation • FWHM(v) < 100 µm • Resources • Lasers, experts, labs …
Some definitions and units Quantity Definition Units Value Flux # photons / unit time Xph/ sec 1012 Fluence flux / unit area (Xph/sec)/ mm 2 1013 Brilliance fluence/ solid angle* Xph/sec/ 1017 (mm 2 -mrad 2) Brightness flux/solid angle* Xph/sec/ mrad 2 1016 * Sometimes defined in terms of bandwidth, e. g. brilliance = (fluence/solid angle)/bandwidth
Which parameters really matter? • For most macromolecular crystallographic experiments fluence is the relevant parameter: we want lots of photons entrained upon a small area • Brilliance matters with very large unit cells where a high divergence is bad
What does high fluence do? • Allows us to get good signal-to-noise from small samples • Allows us to irradiate segments of larger samples to counteract decay • Many experiments per day • Allows us to contemplate experiments we would never consider with lower fluence
What does high brilliance do? • How do we separate spots if the unit cell length > 500 Å? – Back up the detector – Use tiny beams • Large beam divergence will prevent either of those tools from working
Tunability • Monochromatic experiments: We’re allowed to choose the energy that works best for our experiment • Optimized-anomalous experiments: We can collect F(h, k, l) and F(-h, -k, -l) at the energy where they’re most different • Multiwavelength: pick 3 -4 energies based on XAS scan and collect diffraction data at all of them
What energies are available? • Depends on the storage ring • Undulators at big 3 rd-generation sources: 3 -80 Ke. V • Protein experiments mostly 5 -25 Ke. V – Below 5: absorption by sample & medium – Above 25: Edges are ugly, pattern too crowded • Some beamlines still monochromatic
Energy resolution & spectral width • Energy resolution: how selective we can reproducibly produce a given energy – Typically ~ 0. 4 e. V at 3 rd-Gen sources – Need: d. E < [Epeak - Eedge (Se)] ~ 1. 4 e. V • Spectral width: how wide the energy output is with the monochromator set to a particular value
Collimation • Everyone collimates. What’s special? – Beam inherently undivergent – Facility set up to spend serious money making collimation work right • Result: we can match the beam size to the crystal or to a desired segment of it
Resources Storage rings are large facilities with a number of resources in the vicinity • Specialized scientific equipment (lasers) • Smart, innovative people • Sometimes: well-equipped local labs where you can do specialized sample preparations
Why wouldn’t we do this? • Beamtime might still be scarce • You’re away from your home resources • Disruption of human schedules – Travel – 24 -hour to 48 -hour nonstop efforts – Bad or expensive food • Extra paperwork: Safety, facility security, statistics
How does synchrotron crystallography differ from lab crystallography? • Time scale very foreshortened • Multiwavelength means new experimental regimes • Distinct need for planning and prioritizing experiments • Robotics: taking hold faster @ beamlines
How does macromolecular crystallography differ from other beamline activities? • “Physics and chemistry groups at the beamline do experiments; crystallographers do data collection” • Expectation: zero or minimal down-time between users • Often: well-integrated process from sample mounting through structure determination • Typical experimental times short: 10 min/sample, 4 hours / project
Where might we collect data? • SER-CAT: 22 -ID and 22 -BM • SBC-CAT: 19 -BM and 19 -ID • GM/CA-CAT: 23 -ID multiple endstations • NE-CAT: 24 -ID, multiple endstations • LS-CAT: 21 -ID, multiple endstations • Bio. CARS: 14 -BM, 14 -ID
Southeast Regional CAT (22) • Established ~2002 • Run as an academic consortium of about 25 universities, mostly in the southeast, with some legislative or provost-level support • 30% of my salary from there until 2014
GM/CA-CAT (23) • Established around 2004 as a site for NIH GM and Cancer grantees, particularly those working on structural genomics and cancer therapeutics • First APS facility to build out multiple endstations on an insertion device line that are capable of simultaneous use
Bio. CARS • Established around 1997 to do cuttingedge crystallographic projects, particularly involving time-resolved techniques and BSL-2 or BSL-3 samples
SBC-CAT • Oldest macromolecular crystallography facility at the APS • 19 -ID: more structures solved than any other beamline in the world • Good for all sizes and resolutions
LS-CAT • Small consortium of academic labs • Initially funded partly by Michigan government • Built & maintained by Northwestern U • Several endstations: One tunable, the others not • Ample beamtime available
Is travel necessary? • Generally not. Most beamlines have either mail-in or robotic remote access. – Mail-in: user ships samples, local staff collects data – Remote: user ships samples, staff puts puck in robotic Dewar, remote user controls experiment via network • At SER-CAT, over 90% of all data are collected either remotely or via mail-in
Remote & Mail-in Realities • Advantages: – Cheaper – Schedule more flexible – Quicker change-over between users – Less safety-related paperwork • Disadvantages: – At mercy of local staff’s skill – Lose some training opportunities – Less control over experimental details – Remote: requires stable network connection
- Crystallographic directions
- Hexagonal coordinate system
- Crystallographic planes
- Vmse crystallographic planes exercises
- Crystallographic information file
- Hexagonal planes miller indices
- Primative unit cell
- Indices de miller
- Collecting highly parallel data for paraphrase evaluation
- Collecting and displaying data
- Samples of collecting engineering data
- Tubular secretion
- Ductnn
- Lymphatic model
- Corbett maths.com
- Coupon collecting problem
- Collecting gas over water
- Chapter 34 collecting and testing specimens
- Flaplike minivalve
- Collecting gas over water
- Rutherford stamp collecting
- Coin collecting merit badge
- Collect gas over water
- Dr frost maths
- Prize collecting steiner tree