Molecular replacement

Molecular replacement (or MR) is a method of solving the phase problem in X-ray crystallography. MR relies upon the existence of a previously solved protein structure which is homologous (similar) to our unknown structure from which the diffraction data is derived.

The first goal of the crystallographer is to obtain an electron density map, density being related with diffracted wave as follows: ${\displaystyle \rho (x,y,z)={\frac {1}{V}}\sum _{h}\sum _{k}\sum _{l}|F_{hkl}|\exp(2\pi i(hx+ky+lz)+i\Phi (hkl)).}$

With usual detectors the intensity ${\displaystyle I=F\cdot F^{*}}$ is being measured, so all the information about phase (${\displaystyle \Phi }$) is lost. Then, in the absence of phases (Φ), we are unable to complete the shown Fourier transform relating the experimental data from X-ray crystallography (in reciprocal space) to real-space electron density, into which the atomic model is built. MR tries to find the model which fits best experimental intensities among known structures.

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