wwPDB validation report of PDB entry 7ND0

The starting BAM model was created from 5LJO (lateral-open BAM-WT cryoEM structure) with BamA residues 687-700 replaced by those from 5EKQ (crystal structure of BamACDE in a lateral-open conformation). This and 7BM5 (Fab1 crystal structure) were rigid fitted into the BAM-WT Fab1 complex electron density in UCSF Chimera. Molecular dynamics based flexible fitting was then set up in VMD and run in NAMD to fit the structures into the density. The resulting structure was finally real-space refined in phenix to generate the final model.

wild-type beta-barrel assembly machinery (BAM) complex (BamABCDE) bound by a bactericidal Fab fragment

wild-type beta-barrel assembly machinery (BAM) complex (BamABCDE)

Light and heavy chains of bactericidal Fab fragment Fab1

final refinement used the non-uniform refinement in cryoSPARC

half maps from non-uniform refinement were postprocessed in RELION 3.0

Outer membrane protein assembly factor BamA

Outer membrane protein assembly factor BamB

Outer membrane protein assembly factor BamC

Outer membrane protein assembly factor BamD

Outer membrane protein assembly factor BamE

Lateral-closed conformation of the lid-locked BAM complex (BamA E435C S665C, BamBDCE) by cryoEM

Lateral-open conformation of the lid-locked BAM complex (BamA E435C S665C, BamBDCE) by cryoEM

Lateral-open conformation of the POTRA-locked BAM complex by cryoEM

Lateral-open conformation of the lid-locked BAM complex bound by a bactericidal Fab fragment

lateral-open conformation of the wild-type BAM complex (BamABCDE) bound to a bactericidal Fab fragment

Calculated fsc threesigma indicator curve
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)