Stoddard Lab

Stoddard Lab

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Data Collection FAQ

Diffraction pattern of RA-61
Diffraction pattern of RA-61 Image by Lindsey Doyle

What is the current ALS schedule?

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Spring 2023

Please contact Lindsey Doyle (ldoyle@fredhutch.org) to be added to the e-mail list

  • BL 5.0.1    March 2            10am-10pm
  • BL 5.0.2   April 27            10am-10pm
  • BL 5.0.1    May 25             10am-5am
  • BL 5.0.2   June 21            10am-5am

When do crystals ship out for ALS?

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Two days before data collection (i.e. if data collection is on a Thursday then crystals will ship out on Tuesday). Crystals must be loaded into the shipping dewar by 2:30 pm.

How should I acknowledge the ALS for publication and/or structure deposition?

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Updated May 2022

All publications based on work done in whole, or in part, at the ALS/BCSB should include the following acknowledgment:

The Berkeley Center for Structural Biology is supported in part by the National Institutes of Health, National Institute of General Medical Sciences, and the Howard Hughes Medical Institute. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. The Pilatus detector was funded under NIH grant S10OD021832. The ALS-ENABLE beamlines are supported in part by the National Institutes of Health, National Institute of General Medical Sciences, grant P30 GM124169

How should I reference the home source equipment for publication and/or structure deposition?

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S10 instrumentation grant: 1S10OD028581-01

  • X-ray Unit: Rigaku XtalLAB Synergy-R
  • Detector: Rigaku HyPix-6000HE hybride photon counting detector
  • Generator: PhotonJet-R
    • MicroMax-007HF microfocus rotating anode with a Copper source
    • Optics: VHF-style integrated
    • Pixel size: 100 μm
  • Software: CrysAlisPro

How do I schedule time on the home source?

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Sign up on the white boards in the X-ray suite (B3-170).

How do I shut down the home source X-rays in an emergency?

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Hit the large, red EMERGENCY button on the generator’s front panel

What is the wavelength of the home source?

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1.54Å

There’s a blank image where my diffraction should be

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  • If there’s no shadow for the beam stop then...
    • the cover is still on the detector 
    • a water fault alarm has caused the X-rays to turn off (note in this case that the cryo turns off as well so remove your crystal).
  • If there’s a very faint shadow for the beam stop check to make sure X-rays are ramped up to 40 kV/30 mA.
  • If there’s a full shadow for the beam stop then your crystal didn’t diffract. Sorry.

The PC is telling me there’s not enough room to collect a dataset

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All users should be removing their data files at the end of screening/collection. 

Check with other user to see if they can remove any files.

Let Lindsey know so she can schedule a purge.

How do I collect data at 4°C?

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Check with Lindsey: B3-175, x4066, ldoyle@fredhutch.org

We’re out of liquid nitrogen

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Call AirGas at 1-800-224-7427, press 2. Our customer number is 2336490.

The cold nozzle is leaking liquid N2 and/or has an irregular flow

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Turn off the Cryo System overnight

There’s a REALLY loud alarm coming from the back closet

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That’s the cold-water alarm on the Haskris. Let Lindsey in B3-175 know (or Peter in B3-177 if Lindsey isn’t around).

I hit the emergency shut-down button

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Pull out the reset button and turn it clockwise. Turn the power on. Once the run lamp is on and the vacuum is stable, turn on the X-rays and dial them up.

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