2024-12-18 REL PDBe PDBe PDBe 2023-12-19 2024-10-16 2024-10-16 2024-12-18 Max Planck Society Germany European Research Council (ERC) 101116848 European Union REEL analysis reconstructions of lumbricus terrestris erythrocruorin (worm hemoglobin) Pfeil-Gardiner O Murphy BJ stem-eels, eels, reel-em, energy loss, single-particle, elemental mapping, elastic bright field, reconstructed energy loss, METAL BINDING PROTEIN Pfeil-Gardiner O Rosa HVD Riedel D Chen YS Lorks D Kukelhan P Linck M Muller H Van Petegem F Murphy BJ Elemental mapping in single-particle reconstructions by reconstructed electron energy-loss analysis. Nat.Methods US 21 2299 2306 2024 39448878 doi:10.1038/s41592-024-02482-5 1548-7105 EMD-19191 other EM volume Worm hemoglobin Worm hemoglobin 0 1 Lumbricus terrestris singleParticle particle 7.3 C-flat-1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE 100 277.15 FEI VITROBOT MARK IV TFS KRIOS OTHER OTHER FIELD EMISSION GUN 200 50.0 2.7 0.0 0.0 0.0 0.0 80000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
energy filter used in spectroscopy mode, so without a slit
The data were collected as STEM-EELS spectral images.
DECTRIS ELA (1k x 0.5k) 4096 4096 1142 92.0 1
Spectral images were segmented into energy-loss micrographs. Micrographs from the zeroloss region were used for reference reconstruction. Energy-loss reconstructions along the full spectrum were reconstructed with the reconstruction parameters determined with the reference reconstruction.
D6 FOURIER SPACE 27.0 FSC 0.143 CUT-OFF RELION 4.0beta 16648 MAXIMUM LIKELIHOOD RELION 4.0beta
stochastic gradient descent by relion 3D initial model
 MAXIMUM LIKELIHOOD RELION 4.0beta emd_19190.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 132 132 132 0 0 0 132 132 132 481.80002 481.80002 481.80002 90.0 90.0 90.0 X Y Z -0.003047082 0.014324053 0.0005446435 0.0020716998 3.65 3.65 3.65 0.00787 AUTHOR Reference reconstruction emd_19190_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 120 120 120 0 0 0 120 120 120 438.0 438.0 438.0 90.0 90.0 90.0 X Y Z -0.0041623497 0.0038244973 0.000028635552 0.0004301354 3.65 3.65 3.65 AUTHOR Energy-loss map at the carbon K-edge generated by summing REEL-EM maps in the energy range between and 283.2 eV to 287.8 eV. Best displayed with lowpass filtering. emd_19190_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 120 120 120 0 0 0 120 120 120 438.0 438.0 438.0 90.0 90.0 90.0 X Y Z -0.0026781124 0.0026516276 0.000026148613 0.0004436802 3.65 3.65 3.65 AUTHOR Energy-loss map at the oxygen K-edge generated by summing REEL-EM maps in the energy range between and 540.4 eV to 545.0 eV. Best displayed with lowpass filtering. emd_19190_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 120 120 120 0 0 0 120 120 120 438.0 438.0 438.0 90.0 90.0 90.0 X Y Z -0.0037259636 0.0038066744 0.000034783407 0.0005105666 3.65 3.65 3.65 AUTHOR Energy-loss map before the carbon K-edge generated by summing REEL-EM maps in the energy range between and 237.5 eV to 242.1 eV. Best displayed with lowpass filtering. emd_19190_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 132 132 132 0 0 0 132 132 132 481.80002 481.80002 481.80002 90.0 90.0 90.0 X Y Z -0.004105841 0.014270004 0.00045410742 0.0021097208 3.65 3.65 3.65 AUTHOR Halfmap 2 emd_19190_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 132 132 132 0 0 0 132 132 132 481.80002 481.80002 481.80002 90.0 90.0 90.0 X Y Z -0.0041205664 0.014652781 0.0004520153 0.0021130021 3.65 3.65 3.65 AUTHOR Halfmap 1