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Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods.

Terwilliger TC, Berendzen J - Acta Crystallogr. D Biol. Crystallogr. (1999)

Bottom Line: An automated examination of the native Fourier is tested as a means of evaluation of a heavy-atom solution in MAD and MIR methods for macromolecular crystallography.It is found that the presence of distinct regions of high and low density variation in electron-density maps is a good indicator of the correctness of a heavy-atom solution in the MIR and MAD methods.The method can be used to evaluate heavy-atom solutions during MAD and MIR structure solutions and to determine the handedness of the structure if anomalous data have been measured.

View Article: PubMed Central - HTML - PubMed

Affiliation: Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

ABSTRACT
An automated examination of the native Fourier is tested as a means of evaluation of a heavy-atom solution in MAD and MIR methods for macromolecular crystallography. It is found that the presence of distinct regions of high and low density variation in electron-density maps is a good indicator of the correctness of a heavy-atom solution in the MIR and MAD methods. The method can be used to evaluate heavy-atom solutions during MAD and MIR structure solutions and to determine the handedness of the structure if anomalous data have been measured.

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Standard deviation of r.m.s. density as a function of mean phase error in the structure factors used to calculate the map. Amplitudes and phases of structure factors were calculated as in Fig. 1 ▶. Electron-density maps were calculated from these amplitudes and phases after adding random errors to the phases. (a) The standard deviation of r.m.s. density is plotted as a function of the mean phase error using box sizes of 3, 5 and 9 grid units on a side for maps calculated at a resolution of 2.5 Å. (b) The standard deviation of r.m.s. density is plotted as a function of the mean phase error using box size of 5 grid units on a side for maps calculated at resolutions of 2.5, 3.0 and 4.0 Å.
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fig3: Standard deviation of r.m.s. density as a function of mean phase error in the structure factors used to calculate the map. Amplitudes and phases of structure factors were calculated as in Fig. 1 ▶. Electron-density maps were calculated from these amplitudes and phases after adding random errors to the phases. (a) The standard deviation of r.m.s. density is plotted as a function of the mean phase error using box sizes of 3, 5 and 9 grid units on a side for maps calculated at a resolution of 2.5 Å. (b) The standard deviation of r.m.s. density is plotted as a function of the mean phase error using box size of 5 grid units on a side for maps calculated at resolutions of 2.5, 3.0 and 4.0 Å.

Mentions: Fig. 3 ▶(a) illustrates the dependence of the standard deviation of r.m.s. density on the phase error of model maps calculated at a resolution of 2.5 Å. For maps with phase errors greater than about 80°, the standard deviation of r.m.s. density is essentially independent of phase error. For maps with phase errors up to 80°, however, the standard deviation of r.m.s. density decreases uniformly with increasing phase error. The box size used to calculate the standard deviation of r.m.s. electron density appears to have little overall effect on the calculation (compare the curves from boxes with sides 3, 5 and 9 units in Fig. 3 ▶ a).


Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods.

Terwilliger TC, Berendzen J - Acta Crystallogr. D Biol. Crystallogr. (1999)

Standard deviation of r.m.s. density as a function of mean phase error in the structure factors used to calculate the map. Amplitudes and phases of structure factors were calculated as in Fig. 1 ▶. Electron-density maps were calculated from these amplitudes and phases after adding random errors to the phases. (a) The standard deviation of r.m.s. density is plotted as a function of the mean phase error using box sizes of 3, 5 and 9 grid units on a side for maps calculated at a resolution of 2.5 Å. (b) The standard deviation of r.m.s. density is plotted as a function of the mean phase error using box size of 5 grid units on a side for maps calculated at resolutions of 2.5, 3.0 and 4.0 Å.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2746120&req=5

fig3: Standard deviation of r.m.s. density as a function of mean phase error in the structure factors used to calculate the map. Amplitudes and phases of structure factors were calculated as in Fig. 1 ▶. Electron-density maps were calculated from these amplitudes and phases after adding random errors to the phases. (a) The standard deviation of r.m.s. density is plotted as a function of the mean phase error using box sizes of 3, 5 and 9 grid units on a side for maps calculated at a resolution of 2.5 Å. (b) The standard deviation of r.m.s. density is plotted as a function of the mean phase error using box size of 5 grid units on a side for maps calculated at resolutions of 2.5, 3.0 and 4.0 Å.
Mentions: Fig. 3 ▶(a) illustrates the dependence of the standard deviation of r.m.s. density on the phase error of model maps calculated at a resolution of 2.5 Å. For maps with phase errors greater than about 80°, the standard deviation of r.m.s. density is essentially independent of phase error. For maps with phase errors up to 80°, however, the standard deviation of r.m.s. density decreases uniformly with increasing phase error. The box size used to calculate the standard deviation of r.m.s. electron density appears to have little overall effect on the calculation (compare the curves from boxes with sides 3, 5 and 9 units in Fig. 3 ▶ a).

Bottom Line: An automated examination of the native Fourier is tested as a means of evaluation of a heavy-atom solution in MAD and MIR methods for macromolecular crystallography.It is found that the presence of distinct regions of high and low density variation in electron-density maps is a good indicator of the correctness of a heavy-atom solution in the MIR and MAD methods.The method can be used to evaluate heavy-atom solutions during MAD and MIR structure solutions and to determine the handedness of the structure if anomalous data have been measured.

View Article: PubMed Central - HTML - PubMed

Affiliation: Structural Biology Group, Mail Stop M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

ABSTRACT
An automated examination of the native Fourier is tested as a means of evaluation of a heavy-atom solution in MAD and MIR methods for macromolecular crystallography. It is found that the presence of distinct regions of high and low density variation in electron-density maps is a good indicator of the correctness of a heavy-atom solution in the MIR and MAD methods. The method can be used to evaluate heavy-atom solutions during MAD and MIR structure solutions and to determine the handedness of the structure if anomalous data have been measured.

Show MeSH