X-Ray and Neutron Crystal Structure Analysis

Crystal structure analyses by X-ray and to a lesser extent, neutron diffraction, have become increasingly important to the biological sciences over the past decade. We 

For many years it was believed that hydrogen atoms could not be seen in the electron density maps produced by X-ray diffraction. The reason for this is that the atomic X-ray scattering power is proportional to the square of the atomic number. This statement was generally, but not invariably, true until the demise of film-recording methods in the mid-1960 s and the advent of the computer-controlled X-ray diffractometers which could provide very accurate X-ray diffraction intensities. 

A variety of levels of reporting hydrogen atom positions can be found in the literature. These are (1) no hydrogen atomic coordinates reported (in some journals, deposition is required) (2) a selection of hydrogen atomic coordinates are reported. These could be only those which could be calculated from the nonhydrogen positions, or only those observed on the difference maps, or a combination of both (3) all hydrogen coordinates reported (especially in more recent publications). Here again, practices differ. Some authors prefer to report calculated positions when they can be calculated, and observed positions only when they cannot be calculated. 

As the use of low-temperature techniques becomes more routine, the quality of the analyses in this regard should improve, but this will be affected by a trend toward the study of more complex molecules where the diffraction quality of the crystals and the observation-to-parameter ratio becomes less favorable for locating the hydrogen atoms. 

The refinement procedures for hydrogen atoms also vary. Isotropic temperature factors are assigned to the hydrogen atoms, but are generally not refined. They are fixed at the isotropic equivalent values of the anisotropic factors for the atom to which the hydrogen is covalently bonded, or, more appropriately, twice those values. 

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