6OVH | pdb_00006ovh

Cryo-EM structure of Bimetallic dodecameric cage design 3 (BMC3) from cytochrome cb562

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6OT7

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.6389
f_angle_d	0.8697
f_chiral_restr	0.0415
f_plane_restr	0.0066
f_bond_d	0.0058

Sample
Bimetallic dodecameric cage 3 (BMC3)

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	25391
Reported Resolution (Å)	2.6
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	T

Map-Model Fitting and Refinement
Id	1 (6OT7)
Refinement Space	REAL
Refinement Protocol	RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details	Symmetry mates were generated from the atomic model to build the dodecameric cage. Chain IDs were re-assigned to ascend from A-L. The cage PDB was manually fit to the EM density map in UCSF Chimera and refined using phenix.real_space_refine

Data Acquisition
Detector Type	GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU
MODEL FITTING	UCSF Chimera
MODEL REFINEMENT	PHENIX

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
NONE		805156