Ichak rentgenografiyasi: natijani ko'rsatadigan tayyorgarlik

Heavy atom methods (multiple isomorphous replacement ) – If electron-dense metal atoms can be introduced into the crystal, to'g'ridan-to'g'ri usullar yoki Patterson-space methods can be used to determine their location and to obtain initial phases. Such heavy atoms can be introduced either by soaking the crystal in a heavy atom-containing solution, or by co-crystallization (growing the crystals in the presence of a heavy atom). As in MAD phasing, the changes in the scattering amplitudes can be interpreted to yield the phases. Although this is the original method by which protein crystal structures were solved, it has largely been superseded by MAD phasing with selenomethionine.^[128]

Model building and phase refinement

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Structure of a protein alpha helix, with stick-figures for the covalent bonding within electron density for the crystal structure at ultra-high-resolution (0.91 Å). The density contours are in gray, the helix backbone in white, sidechains in cyan, O atoms in red, N atoms in blue, and hydrogen bonds as green dotted lines.^[130]

3D depiction of electron density (blue) of a ligand (orange) bound to a binding site in a protein (yellow).^[131] The electron density is obtained from experimental data, and the ligand is modeled into this electron density.
Qo'shimcha ma'lumotlar: Molekulyar modellashtirish
Having obtained initial phases, an initial model can be built. The atomic positions in the model and their respective Debye-Waller factors (yoki B-factors, accounting for the thermal motion of the atom) can be refined to fit the observed diffraction data, ideally yielding a better set of phases. A new model can then be fit to the new electron density map and successive rounds of refinement is carried out. This interative process continues until the correlation between the diffraction data and the model is maximized. The agreement is measured by an R- omil sifatida belgilangan
qayerda F bo'ladi tuzilish omili. A similar quality criterion is R_ozod, which is calculated from a subset (~10%) of reflections that were not included in the structure refinement. Ikkalasi ham R factors depend on the resolution of the data. Qoida tariqasida, R_ozod should be approximately the resolution in angstroms divided by 10; thus, a data-set with 2 Å resolution should yield a final R_ozod ~ 0.2. Chemical bonding features such as stereochemistry, hydrogen bonding and distribution of bond lengths and angles are complementary measures of the model quality. Phase bias is a serious problem in such iterative model building. Omit maps are a common technique used to check for this.^{[tushuntirish kerak ]}
It may not be possible to observe every atom in the asymmetric unit. Ko'p hollarda, Crystallographic disorder smears the electron density map. Weakly scattering atoms such as hydrogen are routinely invisible. It is also possible for a single atom to appear multiple times in an electron density map, e.g., if a protein sidechain has multiple (<4) allowed conformations. In still other cases, the crystallographer may detect that the covalent structure deduced for the molecule was incorrect, or changed. For example, proteins may be cleaved or undergo post-translational modifications that were not detected prior to the crystallization.