wwPDB validation report of PDB entry 3IZ0

Particles were initially aligned using IHRSR protocol in SPIDER with naked MT as reference. Final reconstruction and CTF correction was performed with FREALIGN. A B-factor of -450 was applied with BFACTOR. FSC was calculated only for MT and Ndc80-NUF2 head, disordered outer head was excluded with soft mask.

80mM PIPES, 1mM MgCl2, 1mM EGTA, 1mM DTT, 0.05% Nonidet P-40, 20uM taxol

2 copies of the Ndc80 bonsai complex bind to each tubulin heterodimer. Ndc80 bonsai is a heterodimer of Ndc80-Spc25 and Nuf2-Spc24 Tubulin is a heterodimer of alpha-beta tubulin
Human Ndc80 bonsai complex bound to the microtubule

objective lens astigmatism corrected at 100Kx mag

2ul of 0.25 mg per ml MTs applied to grid for 1 minute 4ul of 0.7 mg per ml Ndc80 bonsai added, 1 minute manually blotted, then another 4ul of Ndc80 applied 1 minute 2ul removed with pipetter Blot for 2 seconds before plunging, 0mm offset

NDC80-SPC25 chimera protein, Chain B from PDB 2VE7 (Ndc80 bonsai)

NUF2-SPC24 chimera protein, Chain D from PDB 2VE7 (Ndc80 bonsai)

hain B, Beta tubulin from PDB 1JFF hain C, D, Ndc80-SPC25 Chimera from PDB 2VE7, residues 79-437 hain E, F, NUF2-SPC24 Chimera from PDB 2VE7, residues 4-156 (C
Human Ndc80 Bonsai Decorated Microtubule

AUTHORS STATE THAT THE NDC80 COMPLEX FORMS OLIGOMERS ALONG MICROTUBULE PROTOFILAMENTS, BINDING ONCE PER TUBULIN MONOMER. THIS ENTRY CONSISTS OF COORDINATES FOR ONE TUBULIN HETERODIMER BOUND TO A CLUSTER OF 2 NDC80 MOLECULES. THE BINDING SITE IS FORMED BETWEEN TUBULIN MONOMERS, AND THUS THERE IS ONE COMPLETE NDC80-TUBULIN INTERFACE AND ONE NDC80-NDC80 INTERFACE. LARGER CLUSTERS ARE MORE PREVALENT IN VITRO AND ARE LIKELY TO EXIST IN VIVO.

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