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Optimizing structure determination

Optimizing structure determination. How many are we solving? What is the limit? Are we there yet? Why not? What are the biggest problems?. How many are we solving?. http://asdp.bnl.gov/asda/Libraries/pdb_statis/latest/bml/ALS.html. Breaking it down. $$ → photons

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Optimizing structure determination

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  1. Optimizing structure determination How many are we solving? What is the limit? Are we there yet? Why not? What are the biggest problems?

  2. How many are we solving? http://asdp.bnl.gov/asda/Libraries/pdb_statis/latest/bml/ALS.html

  3. Breaking it down $$ → photons photons → data data → models models → results results → $$

  4. Operational Efficiency “representative” 8.3.1 user

  5. Operational Efficiency “representative” 8.3.1 user

  6. Turning data into models 8.3.1 in 2003

  7. Top producing beamlines of the world http://asdp.bnl.gov/asda/Libraries/pdb_statis/latest/bml/ALL.html Structures credited

  8. What is the limit? 28 operating US beamlines ~1011 ph/μm2 exposure limit ÷ 2x109 ph/μm2/s ~ 100,000 datasets/year ÷ 1324 str in 2003 ~ 2% efficient

  9. DVD data archive

  10. Elven Automation Elves examine images and set-up data processing Elves run… mosflm scala solve mlphare dm arp/warp

  11. Elven Automation Apr 6 – 24 at ALS 8.3.1

  12. Elven Automation Apr 6 – 24 at ALS 8.3.1

  13. Why do structures fail? Overlaps Signal to noise Radiation Damage

  14. Ewald sphere avoidable overlaps phi mosaicity detector c* c b a

  15. Ewald sphere unavoidable overlaps phi mosaicity detector c* c a b

  16. Why do structures fail? Overlaps Signal to noise Radiation Damage

  17. MAD phasing simulation mlphare results Correlation coefficient to correct model Anomalous signal to noise ratio

  18. SAD phasing simulation mlphare results Correlation coefficient to correct model Anomalous signal to noise ratio

  19. Minimum required signal (MAD/SAD)

  20. Is it real, or is it MLFSOM?

  21. “We really need those high-resolution spots”

  22. Incremental strategy incremental_strategy.com merged.mtz auto.mat

  23. Why do structures fail? Overlaps Signal to noise Radiation Damage

  24. Distention of cryo with dose before

  25. Distention of cryo with dose after

  26. Water ring shift saturated sucrose in 250mM WO4 0 MGy

  27. Water ring shift saturated sucrose in 250mM WO4 184 MGy

  28. Water ring shift saturated sucrose in 250mM WO4 Photons/s/pixel  7.5 3.8 2.5 1.9 1.5 Resolution (Ǻ)

  29. Protein crystal background

  30. Water ring shift GCN4-p1-N16A trigonal crystal crystal background saturated sucrose Water ring position (Ǻ) Absorbed dose (MGy)

  31. Water ring shift http://www.lsbu.ac.uk/water/amorph.html

  32. Water ring shift bubbles? Richard D. Leapman, Songquan Sun, Ultramicroscopy (1995)

  33. Water ring shift Hydrogen bubbles? Richard D. Leapman, Songquan Sun, Ultramicroscopy (1995)

  34. Water ring shift Hydrogen bubbles? “The hydrogen atom reacts with organic compounds by abstracting H from saturated molecules and by adding to centers of unsaturation, for example, http://www.rcdc.nd.edu/compilations/Rxn.pdf

  35. Damage model system

  36. Data quality vs phasing quality Correlation coefficient Exposure time (min)

  37. Individual atoms decay at different rates Correlation coefficient to observed data Exposure time (min)

  38. Damage changes fluorescence spectrum counts Photon energy (eV)

  39. Damage changes fluorescence spectrum 25mM SeMet in 25% glycerol Exposing at 12680 eV Se cross-section at 12680 eV 0.0 0.2 0.4 0.6 0.8 1.0 Fraction unconverted 0 20 40 60 80 100 120 fluence (103 photons/mm2)

  40. fluorescence probe for damage Wide range of decay rates seen Half-dose = 5.5 ± 0.6 MGy 8 mM SeMet in NaOH Half-dose = 41.7 ± 4 MGy “GCN4” in crystal 0.0 0.2 0.4 0.6 0.8 1.0 Fraction unconverted Protection factor: 660% ± 94% 0 50 100 150 200 Absorbed Dose (MGy)

  41. “Can we do morewith what we’ve got?”

  42. Interleaved Scheduling experiment queue beamline Minor 30s Choe 120s Alberta 60s Alberta 60s Choe 30s Minor 30s

  43. Super Tong SuperTong

  44. SuperTong

  45. “infinite capacity” sample carousel

  46. Carousel open

  47. CHL idlepos

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