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Organism Classification
Alphafold Collection
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Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9BHU
pdb_00009bhu
10.2210/pdb9bhu/pdb
Download file
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
Streptomyces griseus Family 2B encapsulin shell
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Blot force: 20 Blot time: 4 seconds
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
135027
Reported Resolution (Å)
2.71
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Homogeneous refinement with I symmetry imposed, per-particle defocus optimization, per-group CTF parameterization, spherical aberration fit enabled, tetrafoil fit enabled, Ewald sphere correction with negative curvature, and minimize over per-particle scale enabled.
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
127.9
Fitting Procedure
?
Details
An AlphaFold-generated model was fit into the map using ChimeraX v1.5. The model was then refined iteratively by alternating rounds of manual refinement in Coot v8.9.1 and real-space refinements using PHENIX v1.20.1-4487.
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å
2
)
43.22
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
TFS GLACIOS
Minimum Defocus (nm)
1000
Maximum Defocus (nm)
1800
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
?
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
45000
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.4.0+231114
IMAGE ACQUISITION
Leginon
?
CTF CORRECTION
cryoSPARC
4.4.0+231114
MODEL FITTING
UCSF ChimeraX
1.5
MODEL REFINEMENT
Coot
8.9.1
MODEL REFINEMENT
PHENIX
1.20.1-4487
INITIAL EULER ASSIGNMENT
cryoSPARC
4.4.0+231114
FINAL EULER ASSIGNMENT
cryoSPARC
4.4.0+231114
RECONSTRUCTION
cryoSPARC
4.4.0+231114
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?