Stony Brook Integrative Structural Biology Organization Introduction to
Stony Brook Integrative Structural Biology Organization Introduction to Molecular Replacement *Adopted from Eleanor Dodson, MRC LMB TBD LSB 434
Molecular Replacement Background Briefly talk about Patterson function, Rotation, Translation search When can you use molecular replacement Some advantages/disadvantages of molecular
replacement When do you know you have the right solution? Patterson Function Patterson function can be calculated from just
the diffraction data (intensity measurements) Patterson function is the convolution of the electron density on itself i.e. times * The Patterson map can tell us where atoms are relative to one another
THE VECTOR MAP OF TWO ATOMS What is the complete set of vectors between two atoms? There are four vectors, two equal and opposite interatomic vectors and two
self vectors. Vector atom 1 to atom 2 Vector atom 1 to atom 2 Vector atom 1 to atom 1 Vector atom 2 to atom 2
The vector map has a large peak at the origin and two lower peaks on either side of it, separated from the origin by the distance between the
two atoms. Vector map THE VECTOR MAP OF SOME ATOMS We can generate a vector map of a molecule by putting
each atom in succession at the origin molecule Patterson
ROTATION FUNCTION First, consider the model Patterson We put the model in a large P1 box and calculate the Patterson from the structure factors of the model in the P1 box. model in large P1 box
ROTATION? search model Patterson of model in large
P1 box Clusters separated by P1 cell dimensions
ROTATION FUNCTION The Patterson of our unknown structure contains self-vectors and cross-vectors, but because the cell was large, the self-vectors and cross vectors are well separated from one another.
self vector cross vector ROTATION FUNCTION Just as we generated the Patterson for our model in the first orientation, we
can generate the Patterson for the model in any orientation in any sized box. model in same large P1 box in different orientation
Patterson of model in large P1 box in different orientation
ROTATION FUNCTION When the models are in different orientations the Pattersons will not match one another. = X
ROTATION FUNCTION However, when the second model is in the same orientation parts of the Pattersons will match one another, and we can solve the rotation function for the model. =
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