| Literature DB >> 26960126 |
Daniele de Sanctis1, Chloe Zubieta2, Franck Felisaz3, Hugo Caserotto1, Max H Nanao3.
Abstract
Exposure to X-rays, high-intensity visible light or ultraviolet radiation results in alterations to protein structure such as the breakage of disulfide bonds, the loss of electron density at electron-rich centres and the movement of side chains. These specific changes can be exploited in order to obtain phase information. Here, a case study using insulin to illustrate each step of the radiation-damage-induced phasing (RIP) method is presented. Unlike a traditional X-ray-induced damage step, specific damage is introduced via ultraviolet light-emitting diodes (UV-LEDs). In contrast to UV lasers, UV-LEDs have the advantages of small size, low cost and relative ease of use.Entities:
Keywords: RIP; SIR; UV; disulfide bonds; light-emitting diodes; phasing; radiation damage; ultraviolet light
Mesh:
Substances:
Year: 2016 PMID: 26960126 PMCID: PMC4784670 DOI: 10.1107/S2059798315021658
Source DB: PubMed Journal: Acta Crystallogr D Struct Biol ISSN: 2059-7983 Impact factor: 7.652
Figure 1UV-LED support. (a, b) CAD drawings of the support, showing focal cones. (c) Installation on the ID29 beamline at ESRF. The LED light is focused to a spot by the built-in ball lenses. (d) Mechanical drawing of the LED support.
Data-collection statistics
Values in parentheses are for the outer shell.
| Before | Position 2 | Position 3 (after UV) | |
|---|---|---|---|
| Wavelength (Å) | 0.9537 | 0.9537 | 0.9537 |
| Resolution range | 50–1.47 (1.52–1.47) | 50–1.45 (1.50–1.45) | 50–1.52 (1.57–1.52) |
| Space group |
|
|
|
| Unit-cell parameters (Å) |
|
|
|
| Total reflections | 51661 (4682) | 53754 (4963) | 47100 (3746) |
| Unique reflections | 13741 (1319) | 14299 (1368) | 12448 (1137) |
| Multiplicity | 3.7 (3.5) | 3.7 (3.6) | 3.7 (3.3) |
| Completeness (%) | 99.2 (99.2) | 99.3 (99.2) | 99.2 (99.1) |
| Mean | 11.58 (1.84) | 10.03 (2.00) | 11.01 (1.86) |
| Wilson | 26.6 | 26.6 | 27.3 |
|
| 0.038 (0.573) | 0.052 (0.541) | 0.042 (0.5293) |
| CC1/2 | 0.997 (0.673) | 0.994 (0.700) | 0.998 (0.809) |
| Total exposure time (s) | 14.0 | 14.0 | 14.0 |
| Photon flux (photons s−1) | 1.4 × 1011 | 1.4 × 1011 | 1.4 × 1011 |
| Diffraction-weighted X-ray dose (MGy) | 3.19 | 3.76 | 4.34 |
Figure 2Success of SHELXD substructure solution. (a) SHELXD correlation coefficient for all reflections (CCall) versus weak reflections (CCweak) as a function of k. Sets of trial solutions are shown for multiple values of k and are coloured by the best combined figure of merit (CFOM) from that set of trials from blue to red. Note the maximum at k = 0.97789. (b) Post facto comparison of the best substructures from (a) against known substructures. Known substructures are computed by peak-searching a model-phased RIP difference map. The position and relative intensity of the resultant substructure sites are plotted in the xy plane of the unit cell. More intense sites (i.e. sites with the most radiation damage such as the Sγ atoms of some cysteines) are shown as larger circles. This reference substructure is then used to evaluate trial solutions from SHELXD. If a particular site is present in the SHELXD solution the circle is coloured blue, otherwise it is coloured grey. Note that the proportion of found (blue) sites is maximal at at k = 0.97789, like the best CFOMs.
Figure 3Analysis of difference Fourier maps allows the iterative improvement of RIP substructures. As in Fig. 2 ▸, a reference substructure is first computed. However, in this case the presence of negative sites (which come from atoms moving to new positions) is indicated by triangles. At each round of substructure improvement by difference Fourier analysis (indicated in the dark grey bar on the right), minor positive sites, which come from weakly damaged sites (circles) as well as negative sites (triangles), are identified (purple). The size of the shapes are scaled to their relative occupancies.
Figure 4Correlation coefficient (CC) of the partially automatically built structure by SHELXE with native data (black) and figure-of-merit-weighted mean phase error (orange) versus k. Insets: electron-density maps superimposed on the final refined model are shown at several values of k.