1. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

2. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

3. Beam Time Allocation Plexxikon UC Berkeley 25% 5% 10% 8%

4. Beam Time Allocation UC Berkeley 25% 10% 8% 5% 2% Plexxikon General User Program

5. Staff George Meigs Senior Research Associate James Holton Beamline Director Jane Tanamachi Administrator Tom Alber Principal Investigator PRT Member Labs PRT Contractees

6. Staff Group photo?

7. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

8. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

9. Funding for ALS 8.3.1 FY 2006 costTotal costEnd date ContractsU Alberta$200,000$800,00001/07 MD Anderson$116,000$748,00007/08 Plexxikon$150,000$1.25 M02/07 UCSD$35,000$145,0002011 GrantsUCSF NIH Center grant $80,000$320,0006/10 DOE IDAT (SIBYLS)$84,000TBD9/09 NIH STTR (Fluidigm)$28,200$141,0007/08 Total$693,200$3.4 M-

10. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

11. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

12. ADSC Quantum 210 X-ray optics Superbend Plane Parabolic mirror Torroidal mirror Si(111) monochromator Protein Crystal pinhole Scatter guard 2:1 demagnification cancels spherical aberrations comparable flux to a wiggler with < 1% of the heat divergence slits

13. ADSC Quantum 210 X-ray optics Superbend Plane Parabolic mirror Torroidal mirror Si(111) monochromator Protein Crystal pinhole Scatter guard 2:1 demagnification cancels spherical aberrations comparable flux to a wiggler with < 1% of the heat divergence slits

14. Zero-parallax optics pinhole prism microscope Styrofoam™ backlight backstop

15. Zero-parallax optics pinhole prism microscope Styrofoam™ backlight backstop

16. Background scattering at 8.3.1 Resolution (Ǻ) Photons/s/pixel Se edge with detector at 100 mm  7.5 3.8 2.5 1.9 1.5 1.2 1.1

17. Future plan: reduce background Laser machining of cold protein crystal H. Kitano et. al. Jpn. J. Appl. Phys. 44,2 L 54–L 56 (2005)

18. Future plan: optimize samples Laser machining of cold protein crystal H. Kitano et. al. Jpn. J. Appl. Phys. 44,2 L 54–L 56 (2005)

19. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

20. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

21. Safety Management Hardware safety systems Training Safety through simplicity Failsafe envelope Examples: –Liquid nitrogen – better tools –Automatic retraction – eliminate confusion –Automatic backup – eliminate distraction

22. Safety Envelope Radiation Safety System (RSS) Personnel Protection System (PSS) Equipment Protection System (EPS) GERT Training 8.3.1 Training experiment

23. Safety Envelope Radiation Safety System (RSS) Personnel Protection System (PSS) Equipment Protection System (EPS) GERT Training 8.3.1 Training experiment

24. Safety Envelope “There is no safety system that can stop a determined user with a hacksaw” -Anonymous Solution: Create tools that enhance productivity within the safety envelope

25. Example 1: Liquid nitrogen

26. Liquid nitrogen safety concern

27. A safer way

28. Safer and more productive!

29. Example 2: Automatic detector retraction ADSC Quantum 210

31. Detector retraction ADSC Quantum 210

32. Detector retraction ADSC Quantum 210

33. Automatic detector retraction Detector motors are disabled with hutch door open (pinch hazard) Sample is difficult to access with detector in data collection position Common mistake: –forget to retract detector before opening door Result: confusion Solution: –Door will not open with detector forward –Detector automatically retracts on door open attempt

34. March 2003 MOTOROLA and the Stylized M Logo are registered in the US Patent & Trademark Office. All other product or service names are the property of their respective owners. © Motorola, Inc. 2002. Distraction is unsafe! 0.8 1.0 1.2 1.4 1.6 1.8 2468 Distance from the lead vehicle (secs.) Median time to lift foot off accelerator (secs.) Distraction Condition No-Distraction Condition 0.8 1.0 1.2 1.4 1.6 1.8 2468 Distance from the lead vehicle (secs.) Median time to lift foot off accelerator (secs.) Distraction Condition No-Distraction Condition Drivers following a car that suddenly brakes take longer to respond to that event when they are distracted by trying to solve a logic problem. This is especially true if the two vehicles start out close together--when it is critical that the driver in the following vehicle make a rapid response to avoid a rear-end collision.

35. Automated firewire drive backup

36. Automated DVD archive

38. Safety Summary Encourage safe practices by making them the best way to get results Measures are in addition to existing ALS safety envelope Better science and better safety go hand in hand

39. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

40. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

41. Software BLU-ICE 3.0 control system Elves integrated with BLU-ICE ALS-wide beamline health monitor

44. DCS server SSRL DCS 3.0 DHS

45. DCS server SSRL DCS 3.0 at the ALS beamline 8.3.1 Energy Divergence steering Foils plungers lights Detector Collimator beamstop Spindle Goniometer shutter ADSC Q210 detector DHS Wago DHS PMAC1 DHS PMAC2 DHS LabView DHS

46. Touch screen

47. DCS server SSRL DCS 3.0 at the ALS beamline 8.3.1 Energy Divergence steering Foils plungers lights Detector Collimator beamstop Spindle Goniometer shutter ADSC Q210 detector DHS Wago DHS PMAC1 DHS PMAC2 DHS LabView DHS

48. DCS server SSRL DCS 3.0 at the ALS beamline 8.3.1 Energy Divergence steering Foils plungers lights Detector Collimator beamstop Spindle Goniometer shutter ADSC Q210 detector DHS Wago DHS PMAC1 DHS PMAC2 DHS LabView DHS

49. Integration of Elves with BLU-ICE Elves structure solution data collection index Wedger Elves mosflm autoindex strategy most recent image run information

50. Integration of Elves with BLU-ICE Elves structure solution data collection process run information pick un-busy cluster node mosflm scala solve ARP/wARP

51. ALS beamline health monitor

52. ALS lN 2 health monitor

53. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

54. Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity

55. How many are we solving? Jiang & R.M. Sweet (2004)

56. SecondsDescriptionPercent 104490Assigned and available91% 42093Shutter open40% 52684Collecting (3026 images)50% 51806Something else50% Operational Efficiency “representative” 8.3.1 user

57. SecondsDescriptionPercent 51806Something else100% 247s  45 Mounting22% 229s  37 Centering16% 179s  109 Strategizing38% 309s  37 Prepping24% Operational Efficiency “representative” 8.3.1 user

58. NumberDescriptionPercent 446028Images (~7 TB)33% 2346Data sets47% 449MAD/SAD (1:2)19% 48Published2% 8.3.1 in 2003 Turning data into models

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

60. Top producing beamlines of the world http://asdp.bnl.gov/asda/Libraries/pdb_statis/latest/bml/ALL.html x10 6 unique HKLs

61. Top producing beamlines of the world http://asdp.bnl.gov/asda/Libraries/pdb_statis/latest/bml/ALL.html http://biosync.sdsc.edu/ Structures/10 20 photons

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

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

64. Apr 6 – 24 at ALS 8.3.1 Elven Automation 148datasets 117succeded ~3.5 (0.1-75)hours 31 failed ~61 (0-231)hours 2 / 15MAD structures

65. avoiding overlaps c c

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

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

68. Apr 6 – 24 at ALS 8.3.1 Elven Automation 148datasets 117succeded ~3.5 (0.1-75)hours 31failed ~61 (0-231)hours 2 / 15MAD structures

69. “What is a good exposure time?”

70. “How much signal do I need?”

71. Is it real, or is it MLFSOM ?

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

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

74. Minimum required signal (MAD/SAD)

75. SAD phasing experiment Anomalous signal to noise ratio Correlation coefficient to published model

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

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

78. “We have a problem with non-isomorphism”

79. Proteins move

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

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

82. thaw Radiation Damage

83. Lattice damage

84. Distention of cryo with dose before beam

85. Distention of cryo with dose after beam

86. Water ring shift Absorbed dose (MGy) Water ring position (Ǻ) saturated sucrose in 250mM WO4

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

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

89. Specific Damage

91. Individual atoms decay at different rates dose (MGy) Correlation coefficient to observed data 0 12 24 36 48 60

92. Damage changes absorption spectrum Photon energy (eV) counts 1 0

93. fluorescence probe for damage fluence (10 15 photons/mm 2 ) Fraction unconverted 25mM SeMet in 25% glycerol 0.0 0.2 0.4 0.6 0.8 1.0 0 50 100 150 200 250 300 350 400 Exposing at 12680 eV

94. fluorescence probe for damage fluence (10 15 photons/mm 2 ) Fraction unconverted 25mM SeMet in 25% glycerol 0.0 0.2 0.4 0.6 0.8 1.0 0 50 100 150 200 250 300 350 400 Exposing at 12680 eV Se cross-section at 12680 eV

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

96. Scientific highlights