2024-05-15 REL PDBe PDBe PDBe 2023-12-14 2024-05-15 2024-05-15 2024-05-15 Chan Zuckerberg Initiative 2021-234666 United States Max Planck Society Germany Thinner is not always better: Optimising cryo lamellae for subtomogram averaging - Ion-damage layer analysis Tuijtel MW Cruz-Leon S Kreysing JP Welsch S Hummer G Beck M Turonova B In-situ Dictyostelium discoideum ribosome, RIBOSOME Tuijtel MW Cruz-Leon S Kreysing JP Welsch S Hummer G Beck M Turonova B Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging. Sci Adv US 10 eadk6285 eadk6285 2024 38669330 doi:10.1126/sciadv.adk6285 2375-2548 Tuijtel MW Cruz-Leon S Kreysing JP Welsch S Hummer G Beck M Turonova B Thinner is not always better: Optimising cryo lamellae for subtomogram averaging BiorXiv US doi:10.1101/2023.07.31.551274 2692-8205 EMD-19136 other EM volume Ribosome Ribosome 0
Ribosome
Dictyostelium discoideum AX2 cytoplasm 4 subtomogramAveraging cell 6.5 ETHANE 70 20 LEICA EM GP TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 2.5 4.5 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 FEI FALCON IV (4k x 4k) 4096 4096 2 0.24 2.0 1 1 C1 13.7 FSC 0.143 CUT-OFF Warp 1000 261 168000 Template matching Warp MAXIMUM LIKELIHOOD Warp emd_19161.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.3521049 0.9509851 0.027656103 0.14687295 2.446 2.446 2.446 0.297 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 50 nm from lamella surface emd_19161_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.19296564 0.6413179 0.029552395 0.13225402 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 10 nm from lamella surface. emd_19161_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -1.9621775 2.8290427 0.029863141 0.30749065 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 5 nm from lamella surface. Halfmap 1 emd_19161_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -1.9486706 2.4103427 0.029001718 0.29461887 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 5 nm from lamella surface. Halfmap 2 emd_19161_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.15978 0.62048304 0.02943243 0.13137327 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 5 nm from lamella surface. emd_19161_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.1096938 2.5387874 0.030571986 0.3099811 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 10 nm from lamella surface. Halfmap 1 emd_19161_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -1.8998209 2.5744934 0.028532803 0.308356 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 10 nm from lamella surface. Halfmap 2 emd_19161_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.18851566 0.6947507 0.029802544 0.13546076 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 15 nm from lamella surface. emd_19161_additional_8.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.0936854 2.593496 0.029238109 0.33356196 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 15 nm from lamella surface. Halfmap 1 emd_19161_additional_9.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.2176018 2.973156 0.03036698 0.33567432 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 15 nm from lamella surface. Halfmap 2 emd_19161_additional_10.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.20500554 0.77171767 0.02881074 0.13676205 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 20 nm from lamella surface. emd_19161_additional_11.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.1126628 2.925679 0.02765094 0.3570154 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 20 nm from lamella surface. Halfmap 1 emd_19161_additional_12.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.2658138 3.213485 0.02997054 0.34624586 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 20 nm from lamella surface. Halfmap 2 emd_19161_additional_13.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.24721326 0.77588004 0.02897055 0.13850597 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 25 nm from lamella surface. emd_19161_additional_14.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.1358042 2.7136757 0.028954837 0.34741122 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 25 nm from lamella surface. Halfmap 1 emd_19161_additional_15.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.2383242 2.7646053 0.028986266 0.35351014 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 25 nm from lamella surface. Halfmap 2 emd_19161_additional_16.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.22724926 0.798591 0.026131747 0.13884932 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 30 nm from lamella surface. emd_19161_additional_17.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.3657732 2.7878232 0.0258664 0.3619531 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 30 nm from lamella surface. Halfmap 1 emd_19161_additional_18.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.3209755 2.7936099 0.026397094 0.35911536 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 30 nm from lamella surface. Halfmap 2 emd_19161_additional_19.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.33743677 0.9605428 0.02628731 0.14520642 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 35 nm from lamella surface. emd_19161_additional_20.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.287479 3.0365076 0.025318509 0.36802137 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 35 nm from lamella surface. Halfmap 1 emd_19161_additional_21.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.24816 2.8913484 0.027256109 0.3580487 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 35 nm from lamella surface. Halfmap 2 emd_19161_additional_22.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.19129866 0.73400295 0.027592381 0.13678567 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 40 nm from lamella surface. emd_19161_additional_23.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.0965142 2.5648787 0.027691344 0.3459244 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 40 nm from lamella surface. Halfmap 1 emd_19161_additional_24.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.559069 3.0573988 0.027493421 0.38448888 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 40 nm from lamella surface. Halfmap 2 emd_19161_additional_25.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -0.25615984 0.8357069 0.026648998 0.13918379 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 45 nm from lamella surface. emd_19161_additional_26.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.2305763 2.8653185 0.026620423 0.34447497 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 45 nm from lamella surface. Halfmap 1 emd_19161_additional_27.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.515227 2.844789 0.026677575 0.38128477 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 45 nm from lamella surface. Halfmap 2 emd_19161_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.2595878 2.8635352 0.028764509 0.36592358 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 50 nm from lamella surface. Halfmap 1 emd_19161_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 168 168 168 0 0 0 168 168 168 410.928 410.928 410.928 90.0 90.0 90.0 X Y Z -2.317345 2.834946 0.026547696 0.37035477 2.446 2.446 2.446 AUTHOR In-situ ribosome from Dictyostelium discoideum obtained with subtomogram averaging. Ion-damage analysis: 50 nm from lamella surface. Halfmap 2