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PDB Id
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Source Organism
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Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
8E29
pdb_00008e29
10.2210/pdb8e29/pdb
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ELECTRON MICROSCOPY
Sample
Wild-type HsDis3L2 in complex with hairpinC-U12
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
?
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
531561
Reported Resolution (Å)
3.1
Resolution Method
FSC 0.143 CUT-OFF
Other Details
CryoSPARC non-uniform refinement
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
?
Overall B Value
?
Fitting Procedure
?
Details
The model of Homo Sapiens Dis3L2 was used as a starting reference for the protein and the nucleic acid was used from PDB 4PMW. All manual building was done in Coot. The hairpin of the RNA was built by using the dsRNA from PDB 5W0O as a template. The nucleotides were mutated to the sequence of hairpinC-U12. To guide the building of the tetraloop, PDB 1F7Y was used to guide the introduction of restraints in the UUCG tetraloop. All model refinements were done in PHENIX.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å
2
)
62.4
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
700
Maximum Defocus (nm)
2600
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
130000
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
IMAGE ACQUISITION
EPU
2.5
CTF CORRECTION
Warp
1.0.8
MODEL FITTING
Coot
?
INITIAL EULER ASSIGNMENT
cryoSPARC
3.1.0
FINAL EULER ASSIGNMENT
cryoSPARC
3.1.0
CLASSIFICATION
cryoSPARC
3.1.0
RECONSTRUCTION
cryoSPARC
3.1.0
MODEL REFINEMENT
PHENIX
1.18-3855-000
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING ONLY
?
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