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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
8V4Q
pdb_00008v4q
10.2210/pdb8v4q/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Myxococcus xanthus EncA 3xHis pore mutant with tetrahedral symmetry
Specimen Preperation
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 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, 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
Date of Experiment
?
Temprature (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
?
Imaging Experiment
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
?
