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 UC Berkeley 25% 10% 8% 5% 2% Plexxikon General User Program

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

5. Staff Group photo?

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

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

8. 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-

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

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

11. 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

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

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

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

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

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

18. 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

19. Example 1: Liquid nitrogen

20. Liquid nitrogen safety concern

21. A safer way

22. Safer and more productive!

23. Example 2: Automatic detector retraction ADSC Quantum 210

25. Detector retraction ADSC Quantum 210

26. Detector retraction ADSC Quantum 210

27. 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

28. 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.

29. Automated firewire drive backup

30. Automated DVD archive

32. 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 can go hand in hand

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

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

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

38. Touch screen

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

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

41. Apr 6 – 24 at ALS 8.3.1 Elven Automation 27,686images collected 148datasets (15 MAD) 31investigators 56unique cells 5 KDa – 23 MDaasymmetric unit 0.94 – 32 Åresolution (3.2 Å)

42. 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

43. ALS beamline health monitor

44. ALS lN 2 health monitor

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

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

47. AmtB ammonia channel Khademi et. al. (2004) Science 305 1587-94.

48. The E. coli ribosome Schuwirth et. al. (2005) Science 310 827-34

49. DnaA origin-recognition protein Erzberger et. al. (2006) Nat Struct Mol Biol 13, 676-83

50. E. coli rho Skordalakes and Berger (2003) Cell 114, 135

51. multidrug transporter EmrD Yin et. al. (2006) Science 312 741-4

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

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

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

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

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

57. 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

58. avoiding overlaps c c

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

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

61. 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

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

63. Minimum required signal (MAD/SAD)

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

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

66. thaw Radiation Damage

67. Lattice damage

68. Distention of cryo with dose before beam

69. Distention of cryo with dose after beam

70. Specific Damage

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

73. 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%

74. How to improve productivity Nocturnal automation Offline experimental design Understand radiation damage

75. Interleaved Scheduling experiment queuebeamline Minor 30s Choe 120s Alberta 60s Choe 30s Minor 30s

76. cool hand luke

77. “infinite capacity” sample carousel

78. 6-foot conveyor