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Organism Classification
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Search Type
PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
8TNP
pdb_00008tnp
10.2210/pdb8tnp/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
Ternary Complex of DDB1dB:CRBN:pomalidomide with SD40
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
LEICA EM GP
Cryogen Name
ETHANE
Sample Vitrification Details
Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
55205
Reported Resolution (Å)
3.3
Resolution Method
FSC 0.143 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
CC
Overall B Value
102
Fitting Procedure
?
Details
Phenix real-space refinement without rigid body
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å
2
)
53.8
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
TFS TALOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
2000
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
36000
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
Topaz
0.2.5
IMAGE ACQUISITION
SerialEM
4.1b
CTF CORRECTION
cryoSPARC
4.2.0
MODEL FITTING
UCSF ChimeraX
1.5
INITIAL EULER ASSIGNMENT
cryoSPARC
4.2.0
FINAL EULER ASSIGNMENT
cryoSPARC
4.2.0
CLASSIFICATION
cryoSPARC
4.2.0
RECONSTRUCTION
cryoSPARC
4.2.0
MODEL REFINEMENT
PHENIX
1.19.2
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?
