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The atomic structure of the HAdVF-41 penton base in solution
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
21.79
f_angle_d
0.748
f_chiral_restr
0.046
f_bond_d
0.006
f_plane_restr
0.005
Sample
Human adenovirus 41
Specimen Preparation
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
107110
Reported Resolution (Å)
3.8
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
POINT
Point Symmetry
C5
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K2 QUANTUM (4k x 4k)
Electron Dose (electrons/Å**2)
0.93
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
500
Maximum Defocus (nm)
3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
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
Data were collected at a 30 degree tilt of the specimen stage due to a preferred orientation of the sample in the vitrified ice.
EM Software
Task
Software Package
Version
PARTICLE SELECTION
crYOLO
IMAGE ACQUISITION
EPU
CTF CORRECTION
Gctf
1.18
MODEL FITTING
PHENIX
1.18-3845
MODEL REFINEMENT
PHENIX
1.18-3845
INITIAL EULER ASSIGNMENT
RELION
3.1-beta
FINAL EULER ASSIGNMENT
RELION
3.1-beta
CLASSIFICATION
RELION
3.1-beta
RECONSTRUCTION
RELION
3.1-beta
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
NONE
per-micrograph CTF correction as well the initial per-particle CTF correction before 2D classification were performed in GCTF. Later per-particle CTF-refinement were performed in RELION 3.1-beta.