lecture2 - Bioinformatics 2 -- lecture 2 Where do protein...

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Unformatted text preview: Bioinformatics 2 -- lecture 2 Where do protein structures come from? X-ray crystallography What does "resolution" mean? What is a "temperature factor"? NMR What is an "ensemble"? Why so many isotopes? X-ray Crystallography } + Diffraction pattern Electron density map E X-ray e- oscillation scatter X-rays e- has almost zero mass, so it oscillates at the same frequency as the X-rays Oscillating e- emit light in all directions. E e- e- e- e- e- e- e- e- e- t Wavelength: 1.54 Frequency = c/ 2x10 18 s-1 Parallel mirror planes separated by d scatter in phase d n =2d sin Braggs Law: d is the resolution, which depends on and Crystal Planes ...are parallel planes that cut through the origins (dots) of the Unit Cells which make up the crystal. When the crystal planes are positioned like a mirror, with the Bragg angle to the beam, diffraction occurs. (Thats why spots on a diffraction pattern are called reflections.) Each spot on the flm represents a set oF Bragg planes. The amplitude oF each reection is proportional to the variability oF electron density normal to the Bragg planes d 2 Xray beam B r a g g p l a n e s The image of the molecule is reconstructed by superimposing Bragg planes, shifted by phase and scaled by amplitude Each set of parallel lines represents the Bragg planes for one reFection ( one spot on the lm ). From the sum of waves comes an image in 3D. Sir Lawrence Bragg Fitting the model to the density 3D electron density map = electron density at every point in space. Visualized by drawing 3D contours. Since we know the amino acid sequence and we know what the amino acids should look like, we can "ft" a model to the density. 4 parameters are refned For each atom Coordinate refnement Each atom is moved in X,Y and Z until: (1) good stereochemistry is achieved, (2) there is a good match between the atoms and the density. Each atom is assigned a B-Factor or "temperature-factor" , to better ft the density. + x y z B + high B density profle low B density profle the R-Factor Refned coordinates are deposited in the Protein Data Bank : www.rcsb.org Structure quality: R-factor R-factor = (F c- F o )/ (F o ) Free R-factor = R-factor calculated on data not used for renement. Free R is not data not used for renement....
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lecture2 - Bioinformatics 2 -- lecture 2 Where do protein...

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