For AR-NE3A users

  1. External Mode
    The External Mode has been implemented to automate the operation of the MBS and of the Gap after injection of the electron beam. To take advantage of the External Mode, follow the points below.
    • Close the hutch in a safe manner, and turn the key to the EXP position.
    • Push the SHUTTER button to open the DSS (Down Stream Shutter).
    • Push the [External Mode] button on the right side of the STATION CONTROLLER monitor for at least two seconds. The background color will turn blue.
    • When the External Mode is operating, the lights around the key will flash alternately clockwise.

    Please be aware that the External Mode will be canceled when the experimental hutch is opened. It is recommended to use the External Mode when you are going out of the beamline, notably during the beam injection. Furthermore, even when using the External Mode, it is still necessary to wait approximately 5 minutes after the Gap is closed before restarting the experiments, as the beam intensity is not stable immediately after the beam injection.

  2. We started the operation of GPFS.
    The default Working Directory is /gpfs/data/(UserID), as indicated in the UGUI.

  3. Do not close the BBS during your experiments.
    Close the experimental hutch and keep the shutter open if you don't perform experiments for a long time or if you finish your experiments.

  4. Important!!
    When experimenting at AR-NE3A, it is important to remember the injection time of the electron beam into the PF-AR. During the injection, the MBS (Main Beam Shutter) is closed, and the gap of the undulator is opened. As a consequence, you cannot experiment during the injection. After the completion of the injection, you will need to open the MBS and close the gap.
    • An announcement in the experimental hall will confirm the injection. The status displayed at the upper right of the Ring status monitor is going to change according to the following sequence: Acceleration => Injection => Storage => User Run. It takes about 15 minutes for the status to come back to User Run.

    • When the status comes back to User Run, close the hutch (in a safety way), and turn the key to the EXP position (1 in the Figure below).
    • Push the MBS open req. button (2 in the Figure below) to open the MBS. This procedure will take approximately 10 seconds.
      Following opening of the MBS, the Gap should now close automatically.
    • Push the SHUTTER button (3 in the Figure below) to open the DSS (Down Stream Shutter).

    When the beam appears to be too weak, even though all the above steps have been performed correctly, a problem might have occured when closing the Gap.
    As a consequence, please try to close the Gap again manually, as described below.
    • Click the [Gap] button in the Special menu of the beamline control software UGUI.

    • After appearance of the confirmation widget on the UGUI screen, the gap will be closed to a value corresponding to the current wavelength (specified within the UGUI).

Specifications concerning AR-NE3A

Area of Research

Macromolecular Crystallography

Light Source

In-vacuum Undulator (with taper option)


Collimating Mirror
19.2 m
Rhodium coated silicon single crystal
Glancing angle : 3.5 mrad
(Flat shaped, 1000 mm (L) x 80 mm (W) x 70 mm (T) )
20.8 m
Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooled.
Focusing mirror
22.9 m
Rhodium coated SiO2
Glancing angle : 3.5 mrad
(Troidal, 1000 mm (L) x 100 mm (W) x 65 mm (T) )

Photons at Sample Position

Energy range : 0.75 - 1.9 Å
Energy resolution (deltaE / E) : 2.5 x 10-4
Photon Flux : 1.2 x 1012@6.5 GeV, 1.0 Å
Standard slit size (H x V) : 0.20 x 0.17 mm

Facilities in the Experimental Station

X-ray Detector : Pilatus 2M-F
Type : PAD
Detector size : 254 x 289 mm
Pixel size : 172 x 172 µm
Pixel number : 1475 x 1679
Frame data size : 2.5 MByte
Readout time : 0.003 sec.
Detector distance : 80 - 500 mm
Detector vertical offset : 0 - 150 mm
Cryocooling Device : Nitrogen gas flow (95 K ~ 300 K)
Fluorescence Detector : Si-PIN diode

Workstation and Softwares

   5 PC Workstations ( Linux CentOS6 )
   3 PC Windows ( WindowsXP USB2.0 )

Available software for Image Processing : HKL2000, iMosflm, XDS


Improvement of an Automated Protein Crystal Exchange System PAM for High-throughput Data Collection
Masahiko Hiraki, Yusuke Yamada, Leonard M. G. Chavas, Soichi Wakatsuki, Naohiro Matsugaki
"accepted for publication"

Data Management System at the Photon Factory Macromolecular Crystallography Beamline
Yusuke Yamada, Naohiro Matsugaki, Leonard M. G. Chavas, Masahiko Hiraki, Noriyuki Igarashi, Soichi Wakatsuki, Journal of Physics: Conference Series ; 425, 012017 (2013)

Current stats and future prospects of an automated sample exchange system PAM for protein crystallography
Masahiko Hiraki, Yusuke Yamada, Leonard M. G. Chavas, Naohiro Matsugaki, Noriyuki Igarashi, Soichi Wakatsuki, Journal of Physics: Conference Series ; 425, 012014 (2013)

AR-NE3A, a New Macromolecular Crystallography Beamline for Pharmaceutical Applications at the Photon Factory
Yusuke Yamada, Masahiko Hiraki, Kumiko Sasajima, Naohiro Matsugaki, Noriyuki Igarashi, Yasushi Amano, Masaichi Warizaya, Hitoshi Sakashita, Takashi Kikuchi, Takeharu Mori, Akio Toyoshima, Shunji Kishimoto and Soichi Wakatsuki, AIP Conference Proceedings, 1234, 415-418 (2009)

Fully Automated Data Collection Using PAM and the Development of PAM/SPACE Reversible Cassettes
Masahiko Hiraki, Shokei Watanabe, Leonard M. G. Chavas, Yusuke Yamada, Naohiro Matsugaki, Noriyuki Igarashi, Soichi Wakatsuki, Masahiro Fujihashi, Kunio Miki, Seiki Baba, Go Ueno, Masaki Yamamoto, Mamoru Suzuki, Atsushi Nakagawa, Nobuhisa Watanabe, and Isao Tanaka, AIP Conference Proceedings, 1234, 673 (2010)

High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlines
Masahiko Hiraki, Shokei Watanabe, Nobuo pHonda, Yusuke Yamada, Naohiro Matsugaki, Noriyuki Igarashi, Yurii Gaponov and Soichi Wakatsuki, Journal of Synchrotron Radiation, Vol.15, 300-303 (2008)

Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlines
Yusuke Yamada, Nobuo pHonda, Naohiro Matsugaki, Noriyuki Igarashi, Masahiko Hiraki, Soichi Wakatsuki, Journal of Synchrotron Radiation, Vol.15, 296-299,(2008)

Automated Sample Exchange Robots for the Structural Biology Beam Lines at the Photon Factory
Masahiko Hiraki, Shokei Watanabe, Yusuke Yamada, Naohiro Matsugaki, Noriyuki Igarashi, Yurii Gaponov, and Soichi Wakatsuki, AIP Conference Proceedings, 879, 1924 (2007)

Automation in Structural Biology Beamlines of the Photon Factory
Noriyuki Igarashi, Masahiko Hiraki, Naohiro Matsugaki, Yusuke Yamada, Soichi Wakatsuki, Journal of the Crystallographic Society of Japan, Vol.49(6), 359-363 (2007)

Contact Person

Yusuke Yamada (KEK-PF)
Phone : +81-29-864-5642
PHS : +81-29-864-5200 (ext : 4738)
FAX : +81-29-864-2801
E-mail :

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