DOI: 10.5281/zenodo.16752042
title: Experimental charge density of organic nanocrystals revealed by 3D electron diffraction

description: 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