BL4-2 Biological Small Angle Scattering/Diffraction

Data Processing Basics

1. Normalization

    The first step in data processing is to normalize the scattering curves to the incident beam intensity integrated over the x-ray exposure time. This will correct for small flux fluctuations during the measurements.

2. Sample transmission correction

    A sample cell containing a protein solution typically transmits less than 50% of the incident photons due to absorption by water and the window materials.  The transmission of a typical protein solution up to about a few percent (w/v) is practically the same as that of the corresponding solvent solution in the same sample cell.  As long as the same cell is used it is not necessary to correct for sample transmission.  The transmission measurement  requires both the incident beam flux monitor and another flux monitor immediately down stream of the sample. We routinely use a beam stop in which an x-ray photodiode is incorporated for beam transmission measurements.  However, it is usually better to remove the second flux monitor for the scattering measurements in order to eliminate the air gap which will reduce the background scattering.

3. Dead time correction

    The x-ray scattering data is multiplied by a coefficient which depends on the total count rate in case of gas chamber detectors.  Accurate correction to ~100,000 cps is typical.

4. Averaging

    As discussed above, a series of scattering curves is usually recorded to check for time-dependent changes (notably the potential radiation-induced aggregation) in static measurements.  Having confirmed the absence of time-dependent changes, one normally averages the series of scattering curves in order to improve the data statistics.  Error propagation must be taken into account.

5. Background subtraction

    A solvent scattering curve should be processed in the same way as the protein scattering curves, then subtracted channel-by-channel from the corresponding protein scattering curves.

6.  Converting detector channel number to Q(h) or s

    The detector channel or pixel number must be converted to something physically meaningful for data interpretation.  Normally two different quantities are used:

            Q = h = 4psinq/l, where 2q is a scattering angle and l is the wavelength either in Å or nm.

            s = 2sinq/l.  This quantity is equivalent to “inverse D spacing” or “resolution” in crystallography.

We recommend powder samples of either silver behanate or cholesterol myristate, both available at the beam line. The silver behenate is certified by NIST as a standard reference material.

Sample Name
Silver Behenate (IUCr standard) 58.380 Å
Cholesterol Myristate 51.1 Å

References for silver behenate

T. C. Huang et al., "X-ray Powder Diffraction Analysis of Silver Behenate, a Possible Low-Angle Diffraction Standard", J. Appl. Cryst. (1993), 26, 180-184T.

N. Blanton et al., JCPDS-ICDD; Silver Behenate, (1995), Powder Diffraction 10(2), 91-95

T. N. Blanton et al., "Preparation of silver behenate coatings to provide low- to mid-angle diffraction calibration", J. Appl. Cryst. (2000), 33, 172-173

Vendor of Silver Behenate:

The Gem Dugout - Dana E. Smith, 1652 Princeton Drive * State College, PA 16803, Phone: 1-814-238-4069, Fax: 1-814-238-4069, E-mail, Web