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18 results for “3D ED”
Serial synchrotron crystallography dataset and 3D-ED dataset - HEWL crystals obtained by instant crystallization with TbXo4
<h2>Data sets related to the publication "Nucleating Agent Crystallophore Induces Instant Protein Crystallization" by Sauter et al.</h2> <p><em><strong>3D-Electron Diffraction data</strong></em>: The raw data obtained on the protein Hen Egg-White Lysozyme is contained in the file <em>RAW-Data_3D-ED_deposition.tar.bz2</em>.</p> <p>Results of first rounds of model refinement are contained in <em>3D-ED-affi_4-5sets</em> files</p> <p><em><strong>Synchrotron Serial Crystallography data</strong></em>: The raw SSX data obtained on the protein Hen Egg-White Lysozyme can be accessed through <a href="https://doi.org/10.15151/ESRF-DC-1823716276">https://doi.org/10.15151/ESRF-DC-1823716276</a>.</p> <p>Results of first rounds of model refinement are contained in <em>SSX-Xo4-supernatent</em> files</p>
3D ED tilt series of Pigment Red 5
<p>Electron diffraction tilt series of Pigment Red 5. </p> <p><span>The experimental data were acquired using a 200 kV Glacios transmission electron microscope (Thermo Fisher) operating at liquid nitrogen temperature, employing the EPU-D (Thermo Fisher) module in continuous rotation mode. Electron diffraction patterns were collected in nanodiffraction mode, with an effective beam diameter of 1 µm on the sample. Tilt series were acquired within a goniometer tilt range of -60° to 70°, with a frame interval of 1° and a rotation speed of 0.5 s/1°. A binning factor of 4 was applied to the CETA camera, resulting in an effective pixel size of 0.002 </span><span>Å</span><span>^−1.</span></p>
"Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data". Raw data and JANA refinement files.
<p><strong>Chirality and accurate structure models by exploiting dynamical effects in continuous-rotation 3D ED data</strong><br> 3D ED data sets of 5 compounds and JANA refinement files of 12 compounds</p> <p><strong>Relevant tools</strong><strong>:</strong></p> <ul> <li>PETS2: data reduction and analysis of electron diffraction patterns <ul> <li>Download program and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Palatinus, L. <em>et al.</em> Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. <em>Acta Cryst. B</em><strong>75</strong>, 512–522 (2019). <a href="https://doi.org/10.1107/S2052520619007534">DOI: 10.1107/S2052520619007534</a></li> </ul> </li> <li>JANA2006: crystal structure model refinement program <ul> <li>Download program from <a href="http://jana.fzu.cz/">http://jana.fzu.cz/</a> and access step-by-step tutorials at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a></li> <li>Results here were obtained with JANA2006. We recommend using JANA2020.</li> <li>Petricek, V., Dusek, M. & Palatinus, L. Crystallographic Computing System JANA2006: General features. <em>Z. Kristallogr.</em> <strong>229</strong>, 345–352 (2014). <a href="https://doi.org/10.1515/zkri-2014-1737">DOI: 10.1515/zkri-2014-1737</a></li> </ul> </li> <li>DYNGO: Bloch wave program, calculates dynamical diffraction intensities and derivatives <ul> <li>Program automatically included in JANA2006/JANA2020</li> <li>Palatinus, L., Petříček, V. & Corrêa, C. A. Structure refinement using precession electron diffraction tomography and dynamical diffraction: theory and implementation. <em>Acta Cryst. A</em><strong>71</strong>, 235–244 (2015). <a href="https://doi.org/10.1107/S2053273315001266">DOI: 10.1107/S2053273315001266</a></li> </ul> </li> </ul> <p><strong>3D ED data sets:</strong></p> <p>STW_HPM-1 (RT) was measured on a JEOL JEM-2100-LaB6 and diffraction patterns were recorded with an ASI Timepix detector. Another sample of STW_HPM-1 was measured at a temperature of 100 K after cryotransfer with a Titan Krios (CETA-D detector). The other data sets were measured on an FEI Tecnai G2 20 (Olympus SIS Veleta, CCD). Each data set contains the raw diffraction patterns (*.tif) and the basic input files needed to reproduce the data reduction with PETS2 as used in the associated publication (*.pts2, *.celllist, *.cenloc). Step-by-step tutorials are provided for quartz and glycine (and selected steps for abiraterone acetate) at <a href="http://pets.fzu.cz/">http://pets.fzu.cz/</a>.</p> <ul> <li>α-quartz, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>natrolite, stepwise continuous-rotation and precession-assisted (2 data sets from the same crystal)</li> <li>cobalt aluminophosphate (CAP), static ED patterns recorded in 0.1° steps (3 data sets from 2 crystals)</li> <li>abiraterone acetate, stepwise continous-rotation (5 data sets from 5 crystals)</li> <li>STW_HPM-1, continuous-rotation (1 data set, room temperature)</li> <li>STW_HPM-1, continuous-rotation (1 data set, <em>T</em> = 100 K, cryotransfer)</li> </ul> <p><strong>JANA refinement and CIF files:</strong></p> <p>CIF (Crystallographic Information Framework) files include two data items. The first is related to the dynamical and the second to the kinematical refinement. Relevant parameters and statistics specific for dynamical refinement are found in the field _refine_special_details.</p> <p>JANA files are provided for the dynamical and kinematical refinement at the stage after the final refinement cycle together with the original input files generated by PETS2. For quartz and natrolite, relevant files for the refinements against precession-assisted 3D ED data are included. For abiraterone acetate and limaspermidine, relevant files for the absolute structure determination are included.</p> <ul> <li>α-quartz</li> <li>albite</li> <li>mordenite</li> <li>natrolite</li> <li>STW_HPM-1</li> <li>cobalt aluminophosphate (CAP)</li> <li>CAU-36</li> <li>α-glycine</li> <li>carbamazepine</li> <li>(+)-limaspermidine</li> <li>abiraterone acetate</li> <li>MBBF4</li> </ul> <p>For the kinematical refinements based on more than one data set, the self-written tool "CompInt" (unpublished) was used. The tool can be found in the file "tool_scalehkl_compint.zip". Input (*.hkl, *.compint) and output files (*.scalehkl) are provided in the respective folder with the JANA files.</p> <p>Raw data sources of other data sets relevant for the associated publication are given in the SI of the associated publication.</p>
3D ED tilt series of Argyrin D
<p>The electron diffraction tilt series (3D ED) was collected in continuous rotation mode using the dedicated TEM-controlling script (Gorelik at al., 2021). </p> <p>The sample was ultrasonically dispersed in EtOH. A drop of the suspension was placed onto carbon-coated TEM cupper grid. 3D ED data were collected using a Thermofischer TALOS TEM, operated at 200kV (Ulm University). The data were collected at liquid nitrogen temperature. Dry sample was inserted into the TEM and then cooled – no cryo-transfer procedure was applied. Cryo-transfer sample holder allowing for high-tilt goniometer rotation was used. Electron diffraction was performed in nanodiffraction mode with condenser C2 aperture of 50 microns. The effective beam diameter on the sample was about 7 microns. The sample was scanned with the electron dose rate of 0.003 e/A2s, electron diffraction patterns were collected with the dose rate of 0.03 e/A2s. A single dataset within a tilt range of -70…70° containing 118 frames, had a total accumulated dose of 3.5 e/A2. Binning 4 of the CETA camera was used, camera length was 1.35m, resulting in the pixel size of 0.00166 A-1 of 1024x1024 frames, corresponding to the effective detector distance of 1,344 mm. Single frame exposure was 1 second, relative goniometer rotation speed 0.04, resulting in the effective oscillation range of 1.18°.</p> <p>The lateral crystal size was ca. 1.5 micron x 6 micron.</p> <p><em>Gorelik et al., 2021. Acta Cryst. B77, 662–675.</em></p>
3D ED dataset of 1,3,5-triphenylbenzene
<p>Continuous rotation 3D ED data collection of 1,3,5-triphenylbenzene (TPB). See the following table for additional details.</p> <table> <tbody> <tr> <td><strong>Project name</strong></td> <td>TPB_25032024</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td><strong>Instrumental</strong></td> <td> </td> </tr> <tr> <td>Instrument</td> <td>ELDICO <em>ED-1</em> electron diffractometer</td> </tr> <tr> <td>Electron source</td> <td> <p>LaB<sub>6</sub></p> </td> </tr> <tr> <td>Electron energy </td> <td>160 kV</td> </tr> <tr> <td>Wavelength</td> <td>0.02851 Å</td> </tr> <tr> <td>Beam mode</td> <td>pseudo-parallell</td> </tr> <tr> <td>Beam diameter</td> <td>750 nm</td> </tr> <tr> <td>Detector</td> <td>Dectris QUADRO</td> </tr> <tr> <td>Detetor no. of pixels</td> <td>512 x 512</td> </tr> <tr> <td>Detetor pixel size</td> <td>75 µm</td> </tr> <tr> <td>Data collection mode</td> <td>continuous rotation</td> </tr> <tr> <td>Measurement temperature</td> <td>298 K</td> </tr> <tr> <td>Instrument control software</td> <td>eldix, Version 4.3.1</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td><strong>Sample</strong></td> <td> </td> </tr> <tr> <td>Compound</td> <td>1,3,5-triphenylbenzene</td> </tr> <tr> <td>Chemical formula</td> <td> <p>C<sub>24</sub>H<sub>18</sub></p> </td> </tr> <tr> <td>Sample source</td> <td>commercial, 99+% purity</td> </tr> <tr> <td>Grid</td> <td>amorphous carbon on copper</td> </tr> <tr> <td>Sample preparation</td> <td>grinding of the sample between microscope slides and dry preparation on the grid</td> </tr> <tr> <td> </td> <td> </td> </tr> <tr> <td><strong>Files and data formats</strong></td> <td> </td> </tr> <tr> <td>Diffraction frame folders</td> <td>03, 06, 07, 08</td> </tr> <tr> <td>Diffraction frame format</td> <td>.cbf</td> </tr> <tr> <td>Additional files</td> <td>subfolders with STEM images of the particles at different tilt angles</td> </tr> <tr> <td>Comments</td> <td>folder _full.zip contains the full measurement data, folder _recommended.zip already has frames removed which are affected by other crystals in the beam, shadowing by the grid bars, or beam damage</td> </tr> </tbody> </table>
3D ED dataset of co-crystal of GRGDS peptide with trifluoroacetic acid (TFA)
<p>EPU-D electron diffraction dataset of the GRGDS TFA co-crystal. The original diffraction data is in MRC format, with all metadata stored in the PETS2 pts2 file. JANA files for absolute structure determination and dynamical refinement are also included.</p>
Supplementary material 2 from: Koch M, Schulz J, Edgecombe GD (2015) Tentorial mobility in centipedes (Chilopoda) revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 243-267. https://doi.org/10.3897/zookeys.510.8840
Digital image stack used for 3D-reconstruction of the mandibulo-tentorial complex of Hydroschendyla submarina: Explanation note: Series of transverse histological sections from anterior to posterior, provided as movie.
Supplementary material 1 from: Koch M, Schulz J, Edgecombe GD (2015) Tentorial mobility in centipedes (Chilopoda) revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 243-267. https://doi.org/10.3897/zookeys.510.8840
Digital image stack used for 3D-reconstruction of the mandibulo-tentorial complex of Dicellophilus carniolensis: Explanation note: Series of transverse histological sections from anterior to posterior, provided as movie.
3D ED tilt series of PPEA
<p>Data recorded with EPU-D Glacios TEM (Thermofisher) operating at 200 kV in continuous diffraction mode. The tilt sequence starts at -60°, tilt increment 1°, rotation speed 1° per second. Pixel size within the diffraction frames is 0.00098 Å-1, electron beam dimeter on the sample 1.5 µm (nano-electron diffraction mode). Electron dose rate during data collection was 6.016e/nm<sup>2</sup>s, liquid nitrogen temperature was used.</p> <p>2022-06-16-151539_sh_176.3457.mrc - the same dataset, centered and rotated to make the tilt axis run horizontally.</p> <p>2022-06-16-151539_sh_176.3457_SMV.7z, tar - the same dataset in SMV format.</p> <p>MRC2SMV_BS.exe - MRC to SMV converter, written in MatLab, compiled with mcc. Works with the current version (20140?) of EPU-D MRC files. MRC2SMV_BS.exe requires MATLAB Runtime R2018b (9.5), which can be downloaded free of charge from https://de.mathworks.com/products/compiler/matlab-runtime.html</p> <p> </p>
3D ED / MicroED data of BI-3812
<p>The sample was obtained from Boehringer Ingelheim within a frame of opnme project <a href="https://www.opnme.com">https://www.opnme.com</a></p> <p>Electron diffraction tilt series were recorded with GLACIOS TEM (Thermo Fisher) at liquid nitrogen temperature. Measurements were performed using the EPU-D (Thermo Fisher) module in continuous rotation mode with 200 kV electrons (wavelength of 0.0251 Å). Tilt series were collected within ±60° goniometer tilt range with 1° frame interval and rotation speed of 1° per second. The data were collected using an electron dose rate of 6.016 e/nm<sup>2</sup>s. The electron beam size used for diffraction data collection was 1.2 µm. The pixel size within diffraction patterns is 0.001075 Å<sup>-1</sup>.</p>
Original 3D ED datasets of Co DHG and the integrated merged dataset used for structure determination with molecular replacement.
Open the record for dataset details and reuse information.
Figure 5 from: Koch M, Schulz J, Edgecombe GD (2015) Tentorial mobility in centipedes (Chilopoda) revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 243-267. https://doi.org/10.3897/zookeys.510.8840
Figure 5 - Hydroschendyla submarina, selection of micrographs of transverse sections through the head from anterior to posterior. A Section through the anterior head part, showing the mandibulo-tentorial complex at the level of the epipharyngeal bar B Section through the mandibulo-tentorial complex (right side of head) at the level of the junction between epipharyngeal bar and supramandibular arch. C Section through the mandibulo-tentorial complex (left side of head) between the levels shown in B and D. D Section through posterior part of tentorium and mandible (right side of head) at the level of the mesial interconnection of the mandibles by muscle 26. Numbers refer to muscles as listed in Table 1. Abbreviations: br brain cl clypeus, cl-ecr clypeo-epicranial muscle eb epipharyngeal bar of tentorium, ecr epicranium hy hypopharynx lbs labral sidepiece mb mandibular base md mandible mxI first maxilla ph pharynx pp posterior process of tentorium sma supramandibular arch of tentorium sog subesophageal ganglion tb transverse bar of tentorium tmxII telopodite of second maxilla.
Figure 4 from: Koch M, Schulz J, Edgecombe GD (2015) Tentorial mobility in centipedes (Chilopoda) revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 243-267. https://doi.org/10.3897/zookeys.510.8840
Figure 4 - Dicellophilus carniolensis, selection of micrographs of transverse sections through the head from anterior to posterior. A Section through anterior head part in front of the mandibulo-tentorial complex, highlighting muscles arising from the clypeus B Section through the mandibulo-tentorial complex (left side of head) slightly anterior to C; in the inset (scale: 25 µm) the area of flexibility (arrow) between mandibular gnathal lobe and base is magnified. C Section through the mandibulo-tentorial complex (right side of head) at the level of the cuticular tendon (arrow in inset; scale: 25 µm) of the mandibular gnathal lobe. D Section through posterior part of tentorium and mandible (left side of head), showing collagenous tendon system and mandibular septum. Numbers refer to muscles as listed in Table 1. Abbreviations: br brain cl-ecr clypeo-epricranial muscle cl-ep clypeo-epipharyngeal muscle cl-lbr clypeo-labral muscle ct collagenous tendon, ecr epicranium hb hypopharyngeal bar of tentorium lbs labral sidepiece mb mandibular base md mandible mgl mandibular gnathal lobe, mxI first maxilla ph pharynx pp posterior process of tentorium, se septum of mandibular gnathal pouch sma supramandibular arch of tentorium st stilus tb transverse bar of tentorium tmxII telopodite of second maxilla.
Figure 3C from: Koch M, Schulz J, Edgecombe GD (2015) Tentorial mobility in centipedes (Chilopoda) revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 243-267. https://doi.org/10.3897/zookeys.510.8840
Figure 3C - Hydroschendyla submarina, surface model of the left mandibulo-tentorial complex in situ. Click on the image to activate the interactive 3D-mode. (download 3D model)
Figure 3 from: Koch M, Schulz J, Edgecombe GD (2015) Tentorial mobility in centipedes (Chilopoda) revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 243-267. https://doi.org/10.3897/zookeys.510.8840
Figure 3 - Hydroschendyla submarina, surface model of the left mandibulo-tentorial complex. A Medio-frontal view, tentorial muscles 14, 18, and 22b removed as well as hypopharyngeal muscle 25; arrow points to condyle of mandibular gnathal lobe B Oblique dorso-frontal view, extrinsic mandibular muscles 3, 5, and 13 removed as well as tentorial muscles 18 and 22b. Numbers refer to muscles as listed in Table 1. Abbreviations: md mandible tt tentorium.
Figure 2C from: Koch M, Schulz J, Edgecombe GD (2015) Tentorial mobility in centipedes (Chilopoda) revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 243-267. https://doi.org/10.3897/zookeys.510.8840
Figure 2C - Dicellophilus carniolensis, surface model of the left mandibulo-tentorial complex in situ. Click on the image to activate the interactive 3D-mode. (download 3D model)
Figure 1 from: Koch M, Schulz J, Edgecombe GD (2015) Tentorial mobility in centipedes (Chilopoda) revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 243-267. https://doi.org/10.3897/zookeys.510.8840
Figure 1 - Surface model of the mandibulo-tentorial complex, dorsal view onto the left complex within the head capsule (anterior is top). A Dicellophilus carniolensis B Hydroschendyla submarina, tentorial muscles 18 and 22b removed. Numbers refer to muscles as listed in Table 1. Abbreviations: an antenna cl clypeus, ecr epicranium, md mandible, tt tentorium.
Figure 2 from: Koch M, Schulz J, Edgecombe GD (2015) Tentorial mobility in centipedes (Chilopoda) revisited: 3D reconstruction of the mandibulo-tentorial musculature of Geophilomorpha. In: Tuf IH, Tajovský K (Eds) Proceedings of the 16th International Congress of Myriapodology, Olomouc, Czech Republic. ZooKeys 510: 243-267. https://doi.org/10.3897/zookeys.510.8840
Figure 2 - Dicellophilus carniolensis, surface model of the left mandibulo-tentorial complex. A Medio-frontal view, tentorial muscle 14 removed; arrow points to condyle of mandibular gnathal lobe B Oblique dorso-frontal view, extrinsic mandibular muscles removed. Numbers refer to muscles as listed in Table 1. Abbreviations: md mandible tt tentorium.
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