Preparations for Data Reduction

Preparations for Data Reduction
Structural Molecular Biology Laboratory, ChemM230D

Michael R. Sawaya, Duilio Cascio

1) Print out the powerpoint presentation reduce_handouts.ppt and distribute as handouts. You can use print_handouts.com to print the handouts. It takes a long time. Also, you should update studentinstructions_2007.doc and print these current instructions for lab.

Mike's notes for next year: Maybe next time use figure 2.1.3.3 from the International Tables volume F page 52. Also, Table 2.1.3.4 seems crucial. It describes the conditions for the seven crystal systems. It would be good to explain the rotational symmetry of Laue groups, illustrated on page 51.

1.5) Should make a general overall outline of the entire day --360frames->reduced data. A flowchart. Highlight points of spacegroup determination. Get across the idea that we are only integrating under PREDICTED spot locations. Be prepared with xemacs editor. On current handouts, draw a box around the scripts and give them a light gray background.

2) Today we are going to go from 360 raw images to a set of data intensities for each hkl index. It involves 3 steps
A) Assigning an index hkl to each reflection
1) determining the correct Bravais lattice
2) determining and refining the unit cell parameters
3) determining and refining the crystal orientation
B) Integrating the intensities for each reflection
1) summing intensities over a 2 dimensional area
2) summing intensities between films
C) Producing a file containing the integrated intensites for the unique wedge of reciprocal space
1) Test the highest symmetry point group that is consistent with the data
2) Find the set of scale factors for each frame that produces the best agreement between alleged symmetry related intensities.
3) Examining data collection statistics.

At each step, we narrow down the space group of our crystal. From Bravais lattice to Point Group to Space group.

3) Autoindexing -
We have a pattern of spots on film that was produced by diffraction from a crystal. If we knew the orientation of the crystal, the wavelength, the distance between the crystal and the film, and the unit cell parameters, it would be easy to index a reflection on the film. Just look at the sphere of reflection. Trace the diffracted ray back to the reciprocal lattice. The hkl index is equal to the coordinate of the reciprocal lattice point.

The problem is that we are missing nine of the parameters. We dont know the unit cell dimensions or orientation of the crystal.

Look for three repeating intervals of spots. Find the cell with the smallest volume. Show the distortion required to make this cell look like each of the 14 Bravais lattices.

Last week they should have indexed a spot on film using Ewald's sphere diagram I made --mikey_ewald2.gif

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