wwPDB validation report of PDB entry 3J0C

METHOD--all-atom refinement REFINEMENT PROTOCOL--all-atom refinement against cryo-EM density DETAILS--ROSETTA was used to refine the full-length E1 and E2 and all of the structured part of CP. ROSETTA uses the cryo-EM density as a restraint, along with energy minimization, to eliminate steric clashes and assure proper molecular geometry.

After each iteration, the non-icosahedral parts (which included the lipids and the RNA) in the reconstruction were removed by a soft-edged mask derived from an icosahedrally organized, protein-only map that was low-pass filtered to 30 Angstroms. This map then served as the reference model for the next iteration.

CTF parameters were determined from particles within each CCD image

E1-E2-E3-CP complex. The virus contains 240 copies of E1, E2, and capsid proteins
Venezuelan Equine Encephalitis Virus TC-83 Strain

one asymmetric unit of the VEEV contains 4 unique copies of E1, E2, and capsid proteins
Venezuelan Equine Encephalitis Virus TC83 strain E1 protein

one asymmetric unit of the VEEV contains 4 unique copies of E1, E2 and capsid proteins
Venezuelan Equine Encephalitis Virus TC83 strain E2 protein

Venezuelan Equine Encephalitis Virus TC83 strain capsid protein

objective lens astigmatism was corrected at 100,000 times magnification

vitrification carried out in Chiu lab, Houston, TX
2 blots, each blot 2 second before plunging

C-terminal protease domain (UNP residues 114-275)

A cubic portion of the original 3D density map of VEEV (covering one asymmetric unit)

the non-icosahedrally averaged cryo-EM density maps of VEEV

icosahedral asymmetric unit, std point frame
E1 envelope glycoprotein, E2 envelope glycoprotein, Capsid protein (E.C.3.4.21.90)
Models of E1, E2 and CP of Venezuelan Equine Encephalitis Virus TC-83 strain restrained by a near atomic resolution cryo-EM map
geometric validation package for ligand chemistry in protein x-ray structures
20191225.v01 (using entries in the PDB archive December 25th 2019)