Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
High-resolution Cryo-EM of Fab-labeled human parechovirus 3
ELECTRON MICROSCOPY
Sample
Human parechovirus type 3 in complex with fabs from AT12-015
Sample Components
Human parechovirus type 3
fabs from AT12-015
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
HOMEMADE PLUNGER
Cryogen Name
ETHANE
Sample Vitrification Details
We could not control humidity during plunging. It was ambient humidity.
Blot for 1 s before plunging.
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
74927
Reported Resolution (Å)
2.8
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
I
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
Initial model was generated in I-TASSER and SWISSMODEL using 4z92 and 4udf as reference. Initial rigid fit of the model to the map was done in UCSF Ch ...
Initial model was generated in I-TASSER and SWISSMODEL using 4z92 and 4udf as reference. Initial rigid fit of the model to the map was done in UCSF Chimera. Model refinement was done in Coot and MDFF.
Data Acquisition
Detector Type
FEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)
48
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
500
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
75000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
EM Software
Task
Software Package
Version
PARTICLE SELECTION
RELION
2.0
IMAGE ACQUISITION
RELION
2.0
MODEL FITTING
UCSF Chimera
1.12
INITIAL EULER ASSIGNMENT
RELION
2.0
FINAL EULER ASSIGNMENT
RELION
2.0
CLASSIFICATION
RELION
2.1
RECONSTRUCTION
RELION
2.1
MODEL REFINEMENT
MDFF
MODEL REFINEMENT
Coot
0.8.8
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
GCTF was used to estimate ctf
217212
automatic particle selection in RELION using template generated from manually selected particles