Experimental charge density of organic nanocrystals revealed by 3D electron diffraction

This submission contains the data reduction, processing, refinement files, and CIF files related to the experimental charge density analysis of L-tyrosine from three-dimensional electron diffraction (3D ED) data. The dataset includes: Data reduction and processing files from PETS2 (including crystal images) JANA2020 refinement files and CIF files for: o Kinematical IAM refinement o Dynamical IAM refinement o Dynamical multipole model refinement The data was collected using the continuous-rotation 3D ED method. Processing was carried out in PETS2 (1), and structure refinements were performed in JANA2020 (2), incorporating dynamical diffraction theory. The multipole refinement was conducted in a stepwise fashion, beginning with transferred multipole parameters from the MATTS database and followed by iterative refinement of electron population, κ/κ′, and multipole parameters. Hydrogen atom positions and anisotropic displacement parameters were also refined freely. The archive also includes the final CIF files corresponding to each refinement. This dataset supports the results presented in the associated study on applying dynamical multipole refinement to organic molecular crystals and may serve as a reference for future studies on electron density modelling using 3D ED data. All files are organised within a single folder named “L-tyrosine,” containing the relevant PETS2, JANA2020, and CIF files for each refinement mentioned. References: 1. Palatinus, L., et al. Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. Acta Cryst. B75, 512–522 (2019). 2. Petříček, V., Palatinus, L., Plášil, J., Dušek, M., Jana2020 – a new version of the crystallographic computing system Jana. Z. Kristallogr. 238, 271–282 (2023). Parameters L-tyrosine Chemical formula C9H11NO3 Formula weight 181.2 Tilt range, tilt step(deg.) -55 to +30, 0.3 Exposure time per frame(s) 0.4 Flux(e/A2/s) 0.005 Total dose 0.6 Detector distance (mm) 319.00 Temperature (K) 95 Space group P212121 Unit cell a, b, c (Å) 5.8355, 6.8686, 21.1363 Angles α, β, γ (o) 90.0, 90.0, 90.0 Volume (Å-3) 847.18 Resolution full(Å) 0.59 Completeness full/ last shell resolution (%) 90.3/93.2 Redundancy full/ last shell resolution 3.5/3.67 I/s(count) full/ last shell resolution 18.68/3.17 I/s(error model) full/ last shell resolution 3.78/1.55 Rint obs full/ last shell resolution (%) 13.43/12.06 Rint all full/ last shell resolution 16.67/39.32 CC1/2 full/ last shell resolution 97.08/59.97 Total reflections 7994 Unique reflections 2288 Kinematical refinement Reflections used [I >3σ(I)]/all 2140/3999 Constraints/Restraints/Parameters 0/0/163 R1 [I >3σ(I)]/ all (%) 15.20/18.56 wR1 [I >3σ(I)]/ all (%) 21.61/23.67 GooFobs/all 2.29/1.91 Residual potential Max./min. (e Å−1) 0.76/-0.76 Dynamical IAM Refinement Rsg, Dsg 0.66/0 Thickness model wedge Thickness (Å) 3000.74 Tilt correction 0.473 Isotropic mosaicity (°) 0.0001 Reflection used obs [I >3σ(I)]/ all 5708/7864 Constraints/ Restraints/ Parameters 0/0/265 R1obs [I >3σ(I)]/ all (%) 5.30/6.26 wR1obs [I >3σ(I)]/ all (%) 5.74/5.92 No. of reflection after symmetry averaging (obs [I >3σ(I)]/all) 3323/3989 MR1 obs [I >3σ(I)]/ MR1 all /MwR1 all (%) 4.68/5.19/5.28 GooFobs/all 1.80/1.58 Residual potential max./min. (e/Å1) 0.228/-0.245 Dynamical Multipole Refinement Thickness (Å) 3099.52 Tilt correction () 0.492 Isotropic mosaicity (°) 0.0001 Reflection used obs [I >3σ(I)]/ all 5708/7864 Constraints/ Restraints/ Parameters 0/0/348 R1 obs [I >3σ(I)]/ all (%) 4.08/4.99 wR1 obs [I >3σ(I)]/ all (%) 4.30/4.52 No. of reflection after symmetry averaging (obs [I >3σ(I)]/ all) 3323/3989 MR1 obs [I >3σ(I)]/ MR1 all/ MwR1 all (%) 3.50/3.99/3.82 GooFobs/all 1.36/1.21 Residual potential max./min. (e/Å1) 0.147/-0.141