X Ray Facility |
410-413 Kasha Laboratory of Biophysics Off. Phone: 850-644-6448 Institute of Molecular Biophysics Lab. Phone: 850-645-1333 URL:
http://www.sb.fsu.edu/~xray http://www.sb.fsu.edu/~soma |
XRF Instrument Description
X-Ray Facility Instruments & Resources
Updated Oct. 10, 2005
version
Table of contents
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1998-2005 Thayumanasamy Somasundaram
414 Kasha
Laboratory of Biophysics
Institute
of Molecular Biophysics •
E-mail: soma@sb.fsu.edu • URL: http://www.sb.fsu.edu/~soma
Phone
850.644 6448 • Fax 850 644 7244
October 10,
2005
XRF |
|
The X-Ray Facility
is located on the East side of the fourth floor of the newly renovated Kasha
Laboratory of Biophysics (KLB), Institute of Molecular Biophysics (IMB),
Florida State University (FSU) in
The X-Ray Facility has three rotating anode
generators. Two of the three generators
are manufactured by Rigaku Corporation
of
X-Ray Facility has one image plate (IP) detector made in
1992 by Rigaku Corporation of
1) Reusable IPs are based on BaFBr: Eu2+ Photo-Stimulable Luminescence (PSL),
2) The IP with 1900 x 1900 pixel (102 mm/pixel) active area allows continuous data collection with very little dead time between plate swapping,
3) Automated read and erasure of 16 bit/pixel x-ray diffraction data with HeNe laser and erase lamp,
4) Automated analog to digital conversion and export of data to host computer via SCSI interface,
5) High dynamic range (104 to 105, compared to 102 for photographic film), higher sensitivity (102 times more compared to photographic film) and linear response, and
6) The read-out time for 110 mm/pixel size is approximately eight (8) minutes.
X-Ray Facility has one charge coupled device (Mar CCD165) detector
manufactured in 2000 by Mar-USA Inc. of
1) A circular detector with a large (165 mm diameter) x-ray active area consisting of one single CCD chip with no gap between chips,
2) CCD chip is cooled to -70°C using peltier cooler to reduce background noise and dark current,
3) Fast read-out time of 3.5 s for a 2048 x 2048 pixel active area with 78 mm/pixel and 16 bit/pixel, and
4) Small fiber-optic taper (2.7:1) giving good demagnification of the image at the CCD
Both the Rigaku generators are coupled to confocal mirror
systems manufactured by Osmic Inc,
1) It reduces the number of independent alignment parameters making the focusing process faster,
2) It also reduces the number of coupled alignment parameters,
3) Specialized multi-layer mirror coating reduces the contaminating radiation while maximizing the Copper Ka output, and
4) Maximized output flux compared to total reflection mirrors due to larger acceptance- angle and due to the side-by-side geometry of the two mirrors.
We have two cryo cooling systems capable of maintaining the samples at temperatures between 80° and 400° K, with a stability of ±0.1° K. The required temperature can be maintained for several days. The cryo cooling systems (Cryo Stream Model # 600 and 700) manufactured by Oxford CryoSystems of Oxford, England are state of the art instruments with very low liquid nitrogen consumption of 0.6 liter/hour. The details of the cryo system are:
1) Cryo Stream works at ambient pressure making it easier to replenish liquid nitrogen during the run,
2) Very low consumption of liquid nitrogen and the consumption is independent of set temperature.
3) Wide range of cooling and heating rates (360° K/hour to 0.1° K/hour), and
4) Easily programmable to achieve conditions like cycling and holding.
The R-Axis IIc detector sits on top of a variable two-theta stage. This stage allows a wide selection of sample-detector distances anywhere between 65 and 455 mm for a zero 2-theta angle. Non-zero 2-theta angles between -18.00° and +30.00° are achievable for sample-detector distance of at least 120 mm and larger.
Mar CCD detector sits on top of Mar base and allows sample-detector distance anywhere between of 35 and 384 mm for a zero 2-theta angle. Several but limited non-zero 2-theta angles are achievable with this stage for all the sample-detector distances. Mar CCD distance can be controlled remotely with the help of the software.
Oxford CryoStream 700 cryo cooler on the Mar CCD detector
has an automated liquid nitrogen refill system.
This Liquid Level Sensor (Model # 186) manufactured
by American Magnetics Inc. of
A dedicated Pentium III 733 MHz dual processor
We have a 933 MHz Pentium III Linux machine with 21”
monitor, 256 MB memory and 40-gigabyte disk space running Red Hat 7.0 for the processing of home and
synchrotron x-ray diffraction data. This
machine, (raccoon.sb.fsu.edu
| 128.186.103.108) has an internal DDS-5 (aka DAT72) tape drive, an external FireWire DVD-R writer and an
external SCSI DDS-3 tape drive. Another
733
We have two dedicated 3-D stereo-capable workstations for
model building work. One machine (salmon.sb.fsu.edu |
128.186.102.125) runs under Windows XP operating system with 3.01 GHz
In addition, the x-ray facility users have access to a
dual-bootable (Linux or WinXP) IBM ThinkPad laptop computer for synchrotron
trips. This laptop (whisper.sb.fsu.edu
| 128.186.103.114) features a 1.8
Essential and popular data processing and modeling software packages have been installed and licensed in several X-Ray Facility computers. Software packages such as HKL2000, CrystalClear, CCP4, CNS, O, SOLVE, RSREF, and USF are available both at the Facility and Computer Resources workstations. Several of these packages are available both under Linux and/or Windows platforms. Auxiliary software packages such as PYMOL, MOLSCRIPT, ADXV, and XtalView are also available.
For short-term storing and processing of data sets from home
as well as synchrotrons, XRF has a 1 tera byte data storage system (1TB Data Storage). The storage system consists of nine (9) Seagate
Cheetah 10.K7 146 GB Ultra320 SCSI hard drives in RAID
5 (redundant array independent disks, level 5) configuration. Software RAID control, access and data quota
are managed by a dedicated computer (radio.sb.fsu.edu | 128.186.103.112)
running
XRF offers several options for the long-term archiving and storing of the user’s data, ranging from magnetic (DDS & LT01 tapes) and optical (DVD-R and DVD+R) media under both Windows and Linux environments and are shown in Table 1.
Computer |
Operating System |
Interface |
Media |
Capacity (native | compressed) |
|
Seagate STD624000N |
raccoon.sb.fsu.edu (128.186.103.108) |
Linux |
External SCSI |
DDS-3 tape |
12 GB | 24 GB |
Seagate STD1401LW |
spruce.sb.fsu.edu (128.186.103.109) |
Linux |
Internal SCSI |
DDS-4 tape |
20 GB | 40 GB |
Seagate STD1401LW |
anaconda.sb.fsu.edu (128.186.103.102) |
Windows XP SP2 |
Internal SCSI |
DDS-4 tape |
20 GB | 40 GB |
|
raccoon.sb.fsu.edu (128.186.103.108) |
Linux |
Internal SCSI |
DDS-5 |
36 GB | 72 GB |
Pioneer DVR-A04 |
neptune.sb.fsu.edu (128.186.103.106) |
Linux |
External FireWire |
DVD-R & DVD-RW |
~4.5 – 4.7 GB |
Pioneer DVR-A04 |
anaconda.sb.fsu.edu (128.186.103.102) |
Windows XP SP2 |
Internal SCSI |
DVD-R & DVD-RW |
~4.5 – 4.7 GB |
|
radio.sb.fsu.edu (128.186.103.112) |
Linux |
External SCSI |
LTO-1 |
100 | 200 GB |
· Table 1 Data archiving options available at IMB XRF
The data collected at the Facility is currently archived in DDS-4 and DAT72 tapes. Earlier archives were stored in one of the following formats: 4mm DAT tapes, 8mm Exabyte tapes (mostly 8500 or 8500c), ISO 1990 DVD-R, and 4mm DDS-3 tapes.
The facility has several optical and stereo zoom
microscopes for sample screening and mounting.
The Olympus
Model # SZ 60 has
10-63X zoom and a polarizer. The
In addition to above mentioned stereo microscopes, we also
have a Leica
stereo microscope with a Motic digital
camera for crystal documentation. The Leica
S8 APO stereo zoom apochromatic microscope has been interfaced with a 1.3
mega pixel FireWire Motic digital camera and a Windows 2000 computer (phe.sb.fsu.edu |
128.186.103.107). Motic Advanced Imaging 3.2 software allows
automated capture and documentation of crystal images from the microscope. Phe.sb.fsu.edu is under \\XRAY
domain and can be accessed by anyone who has an account in the Windows platform.
A vibration-free constant temperature crystallization chamber is available in room KLB 412 for growing crystals at temperatures different from the ambient and cold room. It has an interior volume of 8 ft3 with wide range of selectable temperature settings (6-25°C).
Cold room dedicated for growing and mounting crystals is located in room KLB 411 adjacent to the Facility.
Dry transport
X-ray facility occupies 1350 ft2 split between the main x-ray lab (KLB 413: 700 ft2), crystal growth room (KLB 412: 270 ft2), cold room (KLB 411; 170 ft2), and office (KLB 414: 140 ft2). The laboratory has access to compressed air, vacuum, and chilled water and UPS power source. The generators are located inside lead glass separators.
We have initiated and installed two internet based devices that constantly monitor the temperature and relative humidity (T & RH) of both the crystallization cold room and the detector area. These networked environmental units from APC allow the Facility users to monitor the current conditions of T & RH of their crystallization areas and warn them via e-mail if the conditions deviate from the set thresholds. We intend to add two more devices to monitor other areas of the XRF.
Single crystal x-ray diffraction data collection can be carried out
in the newly renovated and dedicated 1350 ft2 x-ray facility using
either an automated image plate or a CCD detector. Each detector is coupled to a 5.4 kW copper rotating
anode Rigaku generator with an Osmic Confocal Max-Flux mirror system. The detector’s two-theta stage allows for the
data collection at variety of sample-detector distances as well as offset
detector configuration for high-resolution studies. Special accessories allow for the data collection
at wide range of temperature settings different from the ambient, including
cryo temperatures. Dedicated vibration-free
crystallization chambers and cold room is available for crystal growth and
manipulation at ambient, 4°C, and non-ambient temperatures. Dedicated Linux and Windows based computers
are available for automated data collection and processing of diffraction
data. Essential data manipulation
software packages (HKL, CCP4, O, & CNS) are installed and licensed. Short- and long-term storage of diffraction
data using magnetic (DDS and LT0 tapes) and optical media (CD-R and DVD ± R) are
supported under different operating systems (Linux and Windows). Several mono- and stereo- light microscopes, microscope
with digital camera, cryo
· Figure 1. Schematic drawing of x-ray facility and the East side of fourth floor of IMB (KLB).