SPring-8, the large synchrotron radiation facility

Inquiry number

SOL-0000001068

Beamline

BL41XU (Macromolecular Crystallography I)

Scientific keywords

A. Sample category	biology, medicine, research on method, instrumentation
B. Sample category (detail)	crystal, biomolecule, crystal, protein, pharmaceuticals
C. Technique	X-ray diffraction, absorption and its secondary process, fluorescent X-rays
D. Technique (detail)	single crystal, MAD, XAFS
E. Particular condition	low-T (~ liquid N2)
F. Photon energy	X-ray (4-40 keV)
G. Target information	molecular structure

Industrial keywords

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

Classification

A80.50 Pharmaceuticals, M10.10 single crystal diffraction, M40.10 XAFS

Body text

Multiwavelength anomalous diffraction (MAD) method is the powerful method to obtain the phase information from one sample crystal composed of molecule with heavy atoms.

In this case, the MAD experiments at near energies of iodine K-absorption (33.17 keV) and xenon K-absorption (34.56 keV) were done using third harmonics of undulator on BL41XU.

Sample crystals were prepared from hen egg white lysozyme. Iodine-doped crystals were obtained by co-crystallization with sodium iodide, and xenon-doped crystals were made by putting its under high-pressure (3 MPa.) xenon gas for 15 minutes.

Precise energies of absorption edge of both iodide and xenon were decided by measurement of X-ray absorption spectra from each derivative crystal (Fig. 1). The MAD experiments were done at near energies decided absorption edge, and the phase information of the lysozyme crystal were able to determined from those successfully. Figure 2 shows the positions of iodine and xenon bound to lysozyme molecule.

Figure 1. X-ray absorption spectra from (a) iodine and (b) xenon

Figure 2. Bounding positions of (a) iodine and (b) xenon

[ K. Takeda, H. Miyatake, S.-Y. Park, M. Kawamoto, N. Kamiya, K. Miki, Journal of Applied Crystallography 37, 925-933 (2004), Fig. 2, 5,
©2004 International Union of Crystallography ]

Source of the figure

Original paper/Journal article

Journal title

K. Takeda, et al, J. Appl. Crystallogr. 37, 925-933 (2004)

Figure No.

2, 5

Technique

Multiwavelength anomalous dispersion (MAD) method is that the X-ray diffraction data are collected at near several energies of the absorption edge of heavy atom binding to molecule consisting crystal. By comparing and analyzing those diffraction data, the phase information is decided, and three-dimensional structure is able to determined.

Source of the figure

No figure

Required time for experimental setup

1 hour(s)

Instruments

Instrument	Purpose	Performance
Protein Crystal Diffractometer	To record diffraction data
Peltier-cooled Si-PIN photodiode	To measure X-ray absorption spectrum

References

Document name
K. Takeda, et al. J. Appl. Crystallogr. 37, 925-933 (2004)

Related experimental techniques

Questionnaire

The measurement was possible only in SPring-8. Impossible or very difficult in other facilities.
This solution is an application of a main instrument of the beamline.

Ease of measurement

With a great skill

Ease of analysis

Middle

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

Two-three shifts