wwPDB validation report of PDB entry 6R22

The 4 non-symmetry related copies of the Ty3 Capsid-NTD from the complete capsid shell structure were aligned and averaged to generate a higher resolution 5.5 A structure

yVB1680 strain - BY4741 killer minus, Ty3 null

Cryo-grids containing purified PR- Ty3 particles were imaged in a Titan Krios electron microscope equipped with a Falcon II direct electron detector, operated at 300 kV. Images were collected with a nominal magnification of 75000, giving a pixel size of 1.08 A. Images were collected in integrating mode with a total electron dose of 20 e/A2. The range of applied defocus values was between -1.0 um and -3.5 um.

The sample was applied onto glow-discharged C-flat (Protochips Inc.) holey carbon grids. The grids were blotted from the back side for 11 seconds at room temperature in a chamber at 85% humidity and plunge-frozen into liquid ethane using a manual plunger.

1733 vesicles and near-complete buds were picked from 61 tomograms. Subtomograms were extracted from the surface of the vesicles.

D336I mutation in the active center of the Ty3 protease

Gag3-Pol3,Transposon Ty3-2 TYA-TYB polyprotein

The structure of a Ty3 retrotransposon capsid N-terminal domain dimer

Coatomer subunit alpha, Coatomer subunit epsilon, Coatomer subunit beta, Coatomer subunit beta', Coatomer subunit delta, ADP-ribosylation factor 1, Coatomer subunit gamma-1, Coatomer subunit zeta-1

Author provided fsc threesigma indicator curve

Author provided fsc halfbit indicator curve

Author provided fsc onebit indicator curve

Author provided fsc 0.333 indicator curve

Author provided fsc 0.143 indicator curve

geometric validation package for ligand chemistry in protein x-ray structures

20191225.v01 (using entries in the PDB archive December 25th 2019)