2024-09-25 REL PDBe PDBe PDBe 2023-04-28 2023-12-27 2023-12-27 2024-09-25 Max Planck Society Germany Tomogram of the nucleus of a C. elegans L1 larva Schioetz OH Kaiser CJO Klumpe S Beck F Plitzko JM Caenorhabditis, elegans, nucleus, L1, larva, C. elegans, CYTOSOLIC PROTEIN Schiotz OH Kaiser CJO Klumpe S Morado DR Poege M Schneider J Beck F Klebl DP Thompson C Plitzko JM Serial Lift-Out: sampling the molecular anatomy of whole organisms. Nat.Methods US 21 1684 1692 2024 38110637 doi:10.1038/s41592-023-02113-5 1548-7105 C. elegans L1 larva, CGC strain AM140 C. elegans L1 larva, CGC strain AM140 0 Caenorhabditis elegans AM140 Whole L1 larva tomography tissue 7.5
M9 buffer + 20% Ficoll 400
 Homemade FORMVAR CONTINUOUS 100.0 NITROGEN
High pressure freezing, Leica EM ICE.
Developmentally arrested L1 larvae
OTHER
The value given for _em_high_pressure_freezing.instrument is Leica EM ICE. This is not in a list of allowed values {'LEICA EM HPM100', 'LEICA EM PACT', 'LEICA EM PACT2', 'BAL-TEC HPM 010', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER'} so OTHER is written into the XML file.
 20% Ficoll 400 OTHER OTHER 30 0.03 1800 80 4000 250
Serial Lift-Out of 160000 nm original volume sectioned into 4000 nm slices, thinned to roughly 250 nm. The value given for _em_focused_ion_beam.instrument is TFS Aquilos 2. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.5 4.5 42000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 FEI FALCON IV (4k x 4k) 4096 4096 1 52 2.24 2.0 1 IMOD 4.12.32 56 emd_17248.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 1024 1024 512 0 0 -44 1024 1024 512 12001.28 12001.28 6000.64 90.0 90.0 90.0 X Y Z -2322224.0 2317715.799999999813735 9765.980999999999767 370705.700000000011642 11.72 11.72 11.72 AUTHOR Bin4 nuclear periphery tomogram emd_17248_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 256 0 0 0 512 512 256 12001.28 12001.28 6000.64 90.0 90.0 90.0 X Y Z -5.9232655 7.010239 0.15440154 0.77483976 23.44 23.44 23.44 AUTHOR Bin8 denoised tomogram (cryo-CARE)