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Organism Classification
Alphafold Collection
Indian Data
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Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
9E5E
pdb_00009e5e
10.2210/pdb9e5e/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
Escherichia coli KTE40 DyP peroxidase-loaded encapsulin shell
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Grids were frozen with a blot force of 20, blot time of 4 seconds, 100% humidity, and chamber temperature of 22 degrees C.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
286236
Reported Resolution (Å)
2.17
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Homogeneous refinement was used against an ab-initio map with I symmetry, per-particle defocus optimization enabled, per-group CTF parameter optimization enabled, and Ewald sphere correction enabled using a positive curvature sign.
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
85.5
Fitting Procedure
?
Details
The AlphaFold model was placed using ChimeraX, followed by iterative manual refinement in Coot followed by Phenix real space refinements.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å
2
)
39.91
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
TFS KRIOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
2500
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
105000
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
v.4.1.2
IMAGE ACQUISITION
SerialEM
?
CTF CORRECTION
cryoSPARC
V.4.1.2
MODEL FITTING
UCSF ChimeraX
1.8
INITIAL EULER ASSIGNMENT
cryoSPARC
v.4.1.2
FINAL EULER ASSIGNMENT
cryoSPARC
v.4.1.2
RECONSTRUCTION
cryoSPARC
v.4.1.2
MODEL REFINEMENT
Coot
0.9.8
MODEL REFINEMENT
PHENIX
1.2.1-4487
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?
