Single-crystal 3D electron diffraction dataset collected from ice Ih
Sample: ice micro crystals
Microscope: Thermo Fisher Scientific 200kV Glacios Transmission Electron Microscope (Cryomicroscopy and Electron Diffraction Core Facility at the Centre of New Technologies, University of Warsaw, Poland)
Camera: Ceta-D camera (bin 4x4, rolling shutter, noise reduction mode)
Collection Software: EPU-D (Thermo Fisher), SMV format
Collection Parameters: 200keV, -193°C, 50 μm C2, gun lens 8, spot size 11, extraction voltage 3850V, parallel beam, beam diameter ~1.7 um, beam stop inserted, calibrated camera length 644 mm (670 in UI), oscillation per frame 0.5 deg, 0.5 s exposure time, tilt speed 1.0 deg/s, rotation -55 to +55 deg.
Grid: lacey carbon Cu 200 mesh glow discharged for 60s at 25mA
The data from the above step is stored in the iceRawData.zip file
Data reduction: Data reduction was carried out in CrysAlisPro 1.171.43.68a (Rigaku OD, 2023). Raw .img files from the microscope were imported and converted to .esperanto files. Next peaks on images were identified and indexed, intensities were integrated and corrected, including multi-scan absorption correction. 54 virtual frames were made during data preparation for dynamical refinement.
The data from the data reduction step are stored in the iceCrysAlisDataProcessing.zip file
Kinematical refinements:
Kinematical IAM refinements were performed with Olex2 v. 1.5 using electron scattering parameterization by Peng (1999). Three types of refinement were performed: based on all reflections and with no extinction corrections, based on all reflections and with extinction correction, based on reflection data set from with certain reflections were omitted and with no extinction corrections.
Kinematical HAR refinements were performed using a locally modified version of Olex2. A program based on a development version of the DiSCaMB library was used to generate files with atomic form factors in .tsc format. Clusters of 5 water molecules (‘central’ water molecule and its four nearest neighbours) were to generate local conformations of disordered ice structure. Two possible configurations of water molecules were used in calculations. A second-order Møller–Plesset perturbation theory (MP2) calculation with a cc-pVTZ basis set was used for the calculation of the electron densities. Quantum mechanical calculations were performed with Gaussian. Three types of refinement were performed: based on all reflections and with no extinction corrections, based on all reflections and with extinction correction, based on reflection data set from with certain reflections were omitted and with no extinction corrections.
The data from the kinematical refinement steps are stored in the iceKinematicalIAMandHARrefinementsinOlex2.zip file
Dynamical refinement:
Dynamical IAM refinement was performed with Jana2020 v. 1.3.36 using electron form factors parameterisation from International Tables Vol.C 4.3.1.1. The structure obtained from IAM refinement in Olex2 was used as a starting point. All reflections with the maximal relative excitation error (RSg) equal to 0.4 were included in the refinement. The number of merged frames was set to 6 and the step between frames was set to 4 to obtain virtual frames. A sigma weighting scheme was applied.
The data from the kinematical refinement steps are stored in the iceDynamicalIAMRefinementinJana2020.zip file
(2024-04-17)
