7QV5 | pdb_00007qv5

Amyloid fibril from the antimicrobial peptide uperin 3.5

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	3.636
f_angle_d	0.388
f_chiral_restr	0.056
f_bond_d	0.009
f_plane_restr	0.002

Sample
uperin 3.5

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE-PROPANE
Sample Vitrification Details	wait time 15s after application, blot time 4s

3D Reconstruction
Reconstruction Method	HELICAL
Number of Particles	215020
Reported Resolution (Å)	3
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	HELICAL
Axial Symmetry	C3
Axial Rise	4.86
Angular Rotation	-1.14

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	CC
Overall B Value	59.34
Fitting Procedure
Details	- Initial model building of a single helical layer using ChimeraX and Coot - Expansion to three layers, refinement in ISOLDE - Truncation of outer layers, re-expansion to three layers, refinement using phenix.real_space_refine

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	40

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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	crYOLO	1.8-beta
IMAGE ACQUISITION	EPU	2.8.0.1256
IMAGE ACQUISITION	DigitalMicrograph	3.32.2403
CTF CORRECTION	RELION	3.1.3
MODEL FITTING	UCSF ChimeraX	1.3
MODEL FITTING	Coot	0.9.3
INITIAL EULER ASSIGNMENT	cryoSPARC	2.3
INITIAL EULER ASSIGNMENT	RELION	3.1.3
FINAL EULER ASSIGNMENT	RELION	3.1.3
CLASSIFICATION	RELION	3.1.3
RECONSTRUCTION	RELION	3.1.3
MODEL REFINEMENT	PHENIX	1.19.1
MODEL REFINEMENT	ISOLDE	1.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION	CTF refined after 3D reconstruction	2447463	4 unique helical units per segment