2024-05-15 REL PDBe PDBe PDBe 2018-11-13 2019-02-20 2019-02-20 2024-05-15 German Research Foundation 359471283 Germany Tobacco Mosaic Virus Song B Flegler V TMV, helical virus, coat protein, plant pathogen, VIRUS Song B Lenhart J Flegler VJ Makbul C Rasmussen T Bottcher B Capabilities of the Falcon III detector for single-particle structure determination. Ultramicroscopy NE 203 145 154 2019 30738626 doi:10.1016/j.ultramic.2019.01.002 0304-3991 0953 ULTRDG 6i5a FULLOVERLAP Tobacco mosaic virus Tobacco mosaic virus 0 1 Tobacco mosaic virus Nicotiana sp. 40 180.0 VIRION STRAIN false false Capsid protein Tobacco mosaic virus (strain vulgare) vulgare 0.017636620999999998 1 LEVO MSYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPL VTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTSGPAT P69687 helical helicalArray 10 7.0 Quantifoil R1.2/1.3 COPPER 400 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV
Quantifoil 400 mesh copper grids R 1.2/1.3 were used (Quantifoil Micro Tools GmbH, Jena, Germany). Grids were glow discharged in air at a pressure of 2.2x10-2 Torr for 2 min at medium power with a Harrick Plasma cleaner (PDC-002). Subsequently, 3-4 ul of the sample was pipetted onto the glow discharged grids and plunge frozen in liquid Ethane with a Vitrobot IV (FEI). The sample chamber of the Vitrobot was maintained at 4C and 100% humidity. Wait time between sample application and blotting was 45 s, the drain time 0 s, the blot time 3 s and the blot force 0..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.0 0.58 1.8 2.12 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 79.0 80.0 FEI FALCON III (4k x 4k) INTEGRATING 4096 4096 1 1001 5.0 55.0 1
Movies were motion corrected and exposure weighted either with motioncor2 (see tables 1-3 for details). The defocus was determined for the motion corrected and exposure weighted averages with ctffind4
1 1.39615 22.037 C1 FOURIER SPACE 2.3 FSC 0.143 CUT-OFF RELION 3.0 91927 393692 RELION 3.0
For TMV, some helices were picked manually with the helix picker implemented in relion 2.1. An initial 3D model of these segments was determined using the relion helix option with a cylinder as the starting reference. The aligned helical segments after 3D refinement were subjected to 2D classification without alignment. Three of the 2D class averages were selected as templates for automatic picking of the TMV segments in relion.
Cylinder
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