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Figure 1
Generation of diffraction photographs from an MD trajectory of crystalline lysozyme. (a) The structure of lysozyme solved in-house (tetragonal lattice, 2.1 Å resolution). (b) A 5 × 5 × 5 supercell of crystalline lysozyme in the MD simulation, containing 1000 protein molecules, 391 250 water molecules and 10 000 Cl− ions. (c) Diagram illustrating the calculation of an X-ray diffraction photograph based on the Huygens–Fresnel principle. The red dot represents the position of an atom in the crystal. k and k′ denote wavevectors before and after scattering, respectively. The point p represents a pixel on the receiver plane. (d) A simulated diffraction photograph from a 300 ns MD trajectory of the lysozyme crystal supercell at 298 K. (e) A simulated diffraction photograph from a 300 ns MD trajectory of the lysozyme crystal supercell at 250 K. (f) The experimental diffraction photograph taken at the same crystal rotation angle as the simulated photographs (d) and (e). (g) Flowchart of the structure back-calculation procedure using MD-based simulated diffraction photographs. In brief, the digitized diffraction images in the experimental data files were replaced with the simulated images, and these files were then used as input for the standard pipeline to solve the crystal structure, with our experimentally solved crystal structure as the molecular-replacement model.

IUCrJ
Volume 10| Part 1| January 2023| Pages 16-26
ISSN: 2052-2525
https://doi.org/10.1107/S2052252522011198