8V4Q | pdb_00008v4q

Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry

ELECTRON MICROSCOPY

Starting Model(s)

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

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.777
f_angle_d	0.442
f_chiral_restr	0.043
f_plane_restr	0.004
f_bond_d	0.002

Sample
Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blot force: 5 Blot time: 2 seconds

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	2799588
Reported Resolution (Å)	2.71
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Local refinement of the asymmetric unit containing three copies of the protomer from a starting map with tetrahedral symmetry. The particles used for ...	Local refinement of the asymmetric unit containing three copies of the protomer from a starting map with tetrahedral symmetry. The particles used for refinement were generated by symmetry expansion using tetrahedral symmetry from 233,299 particles.
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Cross-correlation coefficient
Overall B Value	118.3
Fitting Procedure
Details	The starting model was generated using ESMfold then fit into the map using ChimeraX. The placed coordinates were then manually refined using Coot, fol ...	The starting model was generated using ESMfold then fit into the map using ChimeraX. The placed coordinates were then manually refined using Coot, followed by real space refinement in Phenix.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4.2.1
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC	4.2.1
MODEL FITTING	UCSF ChimeraX	1.25
INITIAL EULER ASSIGNMENT	cryoSPARC	4.2.1
FINAL EULER ASSIGNMENT	cryoSPARC	4.2.1
RECONSTRUCTION	cryoSPARC	4.2.1
MODEL REFINEMENT	Coot	0.9.8.1
MODEL REFINEMENT	PHENIX	1.20.1-4487

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		495482

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.