Journal: J Appl Crystallogr / Year: 2016 Title: Modeling truncated pixel values of faint reflections in MicroED images. Authors: Johan Hattne / Dan Shi / M Jason de la Cruz / Francis E Reyes / Tamir Gonen / Abstract: The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated ...The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved refinement of an atomic model against structure factor amplitudes derived from corrected micro-electron diffraction (MicroED) images.
History
Deposition
Feb 20, 2016
Deposition site: RCSB / Processing site: RCSB
Revision 1.0
Jun 8, 2016
Provider: repository / Type: Initial release
Revision 1.1
Jun 22, 2016
Group: Database references
Revision 1.2
Nov 23, 2016
Group: Other
Revision 1.3
Nov 30, 2016
Group: Refinement description
Revision 1.4
Jul 18, 2018
Group: Data collection / Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_sf
ProteinaseK / Endopeptidase K / Tritirachium alkaline proteinase
Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
Conc.: 25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification
Cryogen name: ETHANE
-
Data collection
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
Microscopy
Model: FEI TECNAI F20
Electron gun
Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lens
Mode: DIFFRACTION
Specimen holder
Cryogen: NITROGEN
Image recording
Average exposure time: 4.1 sec. / Electron dose: 0.004 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 184 / Num. of grids imaged: 1 / Num. of real images: 184
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