Experiment: 29KM

ELECTRON MICROSCOPY

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.383
f_angle_d	0.404
f_chiral_restr	0.036
f_plane_restr	0.003
f_bond_d	0.002

Sample
Bacillus subtilis DnaB

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	LEICA EM GP
Cryogen Name	ETHANE
Sample Vitrification Details	Leica EM GP2

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value	139.5
Fitting Procedure
Details	Initial rigid body fitting was done using Chimera X (Fit to Map). After retracing terminal residues, as well as rebuilding around Arg57, further model ...	Initial rigid body fitting was done using Chimera X (Fit to Map). After retracing terminal residues, as well as rebuilding around Arg57, further modelling and real space refinement was used to refine the final model.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	40

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		2578235

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

29KM | pdb_000029km