Atom motions residue number

Mean square fluctuations (MS) of atoms have been used as a useful measure of the internal motions in a protein [13], The total RMS deviation for various significant structures is given in Table 7.3. A plot of the MS deviation as a function of the residue number is shown in Figure 7.3. From a comparison of the starting X-ray structure and the simulated solution data (Figure 7.2(a) dotted and solid lines), one can draw several conclusions. There is a greater apparent degree of movement in the model solution than in the experimental [12] crystalline system. While all simulations show displacement from the X-ray data, some of this movement has also been inferred from solution experiments [2,21]. This can be attributed to several factors. 

The refinement of the overall B results in a significant reduction of all residuals (fourth line in Table 7.3), which is also expected since now we have a realistic global estimate of thermal motions of atoms in the crystal lattice of LaNi4,85Sno.i5. The refined value of the overall atomic displacement parameter is 5 = 1.32(2) A, where the number in parenthesis indicates a standard deviation in the last significant digit. 

Y-Ray crystallography can also be used to obtain dynamic information on conformational oscillations which continually perturb the native conformation. The calculated electron density of any atom in a protein crystal is a time averaged value, dependent on (a) the amount of disorder in the crystal lattice, (b) atomic vibration, and (c) rapid fluctuation between a small number of conformational substates. If the motion between these substates is large then the electron density is smeared and the polypeptide chain cannot be followed, e.g., 80 residues in the citrate (si)-synthase (E.C. 4.1.3.7) structure are like this. Refinement of high-resolution electron... 

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