wwPDB validation report of PDB entry 3J4F

METHOD--Seven hexamers were docked into density then solvated into 1M NaCl. Secondary structure restraints were applied to helices 1 to 11. MDFF was run for 10 ns with symmetry restraints between CA monomers along the chiral axis. The center hexamer was then extracted. PDB entries 3H47 and 2KOD were the starting structures. REFINEMENT PROTOCOL--flexible

(Helical Details: The segments were aligned and reconstructed using Frealign. Twofold symmetry was imposed using IHRSR++.)

With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side and plunge into liquid ethane with a homemade plunger.
With 2.5 uL sample on carbon side, add 3 uL dilution buffer (100 mM NaCl, 50 mM Tris, pH 8.0) to back side. Blot 3-5 seconds from back side.

helical asymmetric unit, std helical frame

Structure of HIV-1 capsid protein by cryo-EM

geometric validation package for ligand chemistry in protein x-ray structures
20191225.v01 (using entries in the PDB archive December 25th 2019)