SPring-8, the large synchrotron radiation facility

Inquiry number

SOL-0000001180

Beamline

BL41XU (Macromolecular Crystallography I)

Scientific keywords

A. Sample category	biology, medicine
B. Sample category (detail)	biomolecule, crystal, protein, nucleic acid, pharmaceuticals
C. Technique	X-ray diffraction
D. Technique (detail)	single crystal
E. Particular condition	low-T (~ liquid He)
F. Photon energy	X-ray (4-40 keV)
G. Target information	molecular structure, local structure, structure analysis, function and structure

Industrial keywords

level 1---Application area	environment, Pharmaceuticals
level 2---Target	catalysis, drug design, process analytical technology (PAT), food
level 3---Target (detail)	protein, drug
level 4---Obtainable information	chemical state, supra-molecular assemblies, absolute configuration
level 5---Technique	diffraction

Classification

A80.50 Pharmaceuticals, A80.60 food、daily necessaries, M10.10 single crystal diffraction

Body text

There are large amount of water molecules in a protein crystal, and these are changed to hydroxyl radicals by X-ray exposure. It is thought that X-ray damages are caused by diffusing of those radicals while destroying the tertiary structure of the protein or intermolecular interaction in the crystal. X-ray damage is observed as a decrease in the X-ray diffraction ability, a deterioration of diffraction spots or an increase of mosaic spread. These prevent a precise data collection. Cooling the sample about to 100K is effective in the decrease of X-ray damage to prevent radicals from diffusing.

In the X-ray diffraction experiment using generator in laboratory or bending magnet beamline in past facilities, X-ray damage was hardly observed by cooling samples to 100K. However, X-ray damage was occurred in 100K using beamlines at third-generation synchrotron facilities.

In this case, sufficient diffraction data could not be collected in 100K by X-ray damage. Then, the sample was cooled to 35K by helium gas flow cryostream cooler, and precise diffraction data sets of ArcTGT・tRNA^Val complex from P.horikoshii were collected successfully.

By analyzing these data, form of tRNA was newly discovered (Fig. 1).

Figure 1. Drawings of newly discovered form (A) and conventional L form (B)of tRNA

[ R. Ishitani, O. Nureki, N. Nameki, N. Okada, S. Nishimura and S. Yokoyama, Cell 113, 383-394 (2003), Fig. 3,
©2003 Cell Press ]

Source of the figure

Original paper/Journal article

Journal title

R. Ishitani, et al., Cell 113, 383-394 (2003)

Figure No.

3

Technique

Source of the figure

No figure

Required time for experimental setup

3 hour(s)

Instruments

Instrument	Purpose	Performance
Protein Crystal Diffractometer	To record diffraction data
Helium gas flow cryostream cooler	To cool sample

References

Document name
R. Ishitani, et al., Cell 113, 383-394 (2003)

Related experimental techniques

Questionnaire

This solution is an application of a main instrument of the beamline.

Ease of measurement

Middle

Ease of analysis

Middle

How many shifts were needed for taking whole data in the figure?

Four-nine shifts