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Title: Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser (CXIDB ID 30)

This dataset contains the diffraction patterns that were used for the first three-dimensional reconstruction of a virus using FEL data. The sample was the giant mimivirus particle, which is one of the largest known viruses with a diameter of 450 nm. The dataset consists of the 198 diffraction patterns that were used in the analysis.
Authors:
Publication Date:
Report Number(s):
CXIDB ID 30
DOE Contract Number:
AC02-05CH11231
Product Type:
Dataset
Research Org(s):
Coherent X-ray Imaging Data Bank (Lawrence Berkeley National Laboratory); Uppsala University, SLAC National Accelerator Laboratory, Yale University, Diamond Light Source, Lawrence Berkeley National Laboratory
Sponsoring Org:
Uppsala University, SLAC National Accelerator Laboratory, Yale University, Diamond Light Source, Lawrence Berkeley National Laboratory
Resource Relation:
Related Information: Three-Dimensional Reconstruction of the Giant Mimivirus Particle with an X-Ray Free-Electron Laser, Tomas Ekeberg et al. Physical Review Letters, 2015, http://dx.doi.org/10.1103/PhysRevLett.114.098102
Subject:
Mimivirus; XFEL; AMO; Single Particle X-ray Diffraction Imaging; X-ray Free-electorn Lasers; LCLS
OSTI Identifier:
1236752
  1. The Coherent X-ray Imaging Data Bank (CXIDB) is a new database which offers scientists from all over the world a unique opportunity to access data from Coherent X-ray Imaging (CXI) experiments. The main goal of the Coherent X-ray Imaging Data Bank is to create an open repository for CXI experimental data. CXIDB is dedicated to further the goal of making data from Coherent X-ray Imaging (CXI) experiments available to all, as well as archiving it. The website also serves as the reference for the CXI file format, in which most of the experimental data on the database is stored in.
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  1. These 2000 single-shot diffraction patterns include were either background-scattering only or hits (background-scattering plus diffraction signal from sub-micron ellipsoidal particles at random, undetermined orientations). Candidate hits were identified by eye, and the remainder were presumed as background. 54 usable, background-subtracted hits in this set (proceduremore » in referenced article) were used to reconstruct the 3D diffraction intensities of the average ellipsoidal particle. « less
  2. This dataset consists of 79,992 diffraction patterns stored in cbf format. A step-by-step tutorial on the reconstruction of the Bragg intensities using the EMC algorithm (Loh & Elser 2009) is described [here](https://github.com/tl578/EMC-for-SMX/wiki). We thank the authors of Martin-Garcia et al. (2017) for their gracious accessmore » to the data. Reduced data files: For those who would like to try an EMC reconstruction immediately, the data reduction step can be skipped by downloading the reduced data files provided by us. See [here](https://github.com/tl578/EMC-for-SMX/wiki/Data-reduction#skipping-data-reduction) for more details. « less
  3. These are the files used to reconstruct the images in the paper "Single Mimivirus particles intercepted and imaged with an X-ray laser". Besides the diffracted intensities, the Hawk configuration files used for the reconstructions are also provided. The files from CXIDB ID 1 are themore » pattern and configuration files for the pattern showed in Figure 2a in the paper. « less
  4. These are the files used to reconstruct the images in the paper "Single Mimivirus particles intercepted and imaged with an X-ray laser". Besides the diffracted intensities, the Hawk configuration files used for the reconstructions are also provided. The files from CXIDB ID 2 are themore » pattern and configuration files for the pattern showed in Figure 2b in the paper. « less
  5. This dataset is a derivative product of raw meteorological data collected at Barro Colorado Island, Panama (see acknowledgements below). This dataset contains the following: 1) a seven-year record (2008-2014) of meteorological observations from BCI that is in a comma delimited text format, 2) an R-scriptmore » that converts the observed meteorology into an hdf5 format that can be read by the ED2 model, 3) two decades of meteorological drivers in hdf5 format that are based on the 7-year record of observations and include a synthetic 2-yr El Nino drought, 4) a ReadMe.txt file that explains how the data in the hdf5 meteorological drivers correspond to the observations. The raw meteorological data were further QC'd as part of the NGEE-Tropics project to derive item 1 above. The R-script makes the appropriate unit conversions for all observed meteorological variables to be compatible with the ED2 model. The R-script also converts RH into specific humidity, splits total shortwave radiation into its 4-stream parts, and calculates longwave radiation from air temperature and RH. The synthetic El Nino drought is based on selected months from the observed meteorology where in each, precipitation (only) of the selected months was modified to reflect the precipitation patterns of the 1982/83 El Nino observed at BCI. « less