The dataset contains 3D Fourier maps of electrostatic potential and electron density for proteinase K generated with the transferable aspherical atom model (TAAM) using the UBDB/MATTS data bank, the associated structural model of proteinase K and structure factors files.
For the technical details on the method to generate the Fourier maps of electrostatic potential and electron density and for the theoretical background on the method, see (Kulik et al., 2022).
The Fourier maps were generated using the atomic coordinates and B-factors from the model of proteinase K structure from Parengyodontium album (PDB ID 5i9s (Hattne et al., 2016)). The LSDB program (Volkov et al., 2004) was used to automatically assign the UBDB2018 atom type parameters (Kumar et al., 2019) to all atoms. DiSCaMB library, available at http://4xeden.uw.edu.pl/software/ (Chodkiewicz et al., 2018), was used to calculate the structure factors for X-ray diffraction for the TAAM with UBDB2018 parameters at given resolution and then to convert them to the structure factors for electron diffraction using the Mott-Bethe formula. The 3D Fourier maps of electrostatic potential (eTAAM) and electron density (xTAAM) were generated using the WinXD2016 package (Volkov et al., 2016) XDFOUR module at resolutions from 1 Å to 4 Å every 1 Å, and with voxel size 0.3 Å. The maps were generated in two versions: with or without taking into account the thermal smearing effects (denoted as with B or without B, respectively). The same set of B-factors was applied at every resolution in the Fourier maps that include the thermal smearing effects. The 3D Fourier maps deposited here were trimmed with a 3 Å margin around the protein and were not scaled. The associated structural model of proteinase K contains hydrogen atoms and B-factors as used for all the calculations.
The structure factors files feature seven columns. The first three columns correspond to the reflection indices up to 1 Å resolution. Next, there are two sets of Fourier coefficients. The first two coefficients correspond to the real and imaginary parts of the TAAM structure factors, respectively. Additionally, we provide the second set of coefficients that correspond to the real and imaginary parts of the IAM structure factors. The structure factors files make it possible to generate the 3D Fourier maps of electrostatic potential and electron density calculated with TAAM or IAM, with or without taking into account the thermal smearing effects (denoted as with B or without B, respectively) at any given resolution worse than or equal to 1 Å.
References:
Kulik, M., Chodkiewicz, M. L. & Dominiak, P. M. (2022). Acta Crystallographica Section D, 78(8), 1010–1020.
Hattne, J., Shi, D., de la Cruz, M. J., Reyes, F. E. & Gonen, T. (2016). J Appl Crystallogr, 49(Pt 3), 1029–1034.
Volkov, A., Li, X., Koritsanszky, T. & Coppens, P. (2004). J. Phys. Chem. A, 108, 4283–4300.
Kumar, P., Gruza, B., Bojarowski, S. A. & Dominiak, P. M. (2019). Acta Crystallogr A Found Adv, 75(Pt 2), 398–408.
Chodkiewicz, M. L., Migacz, S., Rudnicki, W., Makal, A., Kalinowski, J. A., Moriarty, N. W., Grosse-Kunstleve, R. W., Afonine, P. V., Adams, P. D. & Dominiak, P. M. (2018). J Appl Crystallogr, 51(Pt 1), 193–199.
Volkov, A., Macchi, P., Farrugia, L. J., Gatti, C., Mallinson, P., Richter, T. & Koritsanszky, T., (2016). XD2016 - a computer program package for multipole refinement, topological analysis of charge densities and evaluation of intermolecular energies from experimental and theoretical structure factors.
(2025-01-27)
