Experiment: 21BQ

ELECTRON MICROSCOPY

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other	Other

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.911
f_angle_d	0.453
f_chiral_restr	0.035
f_bond_d	0.005
f_plane_restr	0.002

Sample
Ex vivo Sup35 prion fibrils from yeast carrying strong [PSI+] variant

Specimen Preparation
Sample Aggregation State	FILAMENT
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

Map-Model Fitting and Refinement
Id	1
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target	Maximum likelihood with map correlation
Overall B Value	59.7
Fitting Procedure
Details	A single protomer was built de novo into the sharpened map in Coot, with unambiguous sequence assignment. The built protomer was stacked into a five-l ...	A single protomer was built de novo into the sharpened map in Coot, with unambiguous sequence assignment. The built protomer was stacked into a five-layer segment by rigid-body placement in UCSF Chimera, and the resulting model was refined in PHENIX real-space refine with NCS constraints between the five chains and individual ADPs.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	52

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	700
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	0.01
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	81000
Calibrated Magnification	57937
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details	Cs corrected, 3x3 holes (2 exposures per hole) image-shift data acquisition strategy

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1259000	Filaments were automatically picked with crYOLO using an inter-box step of 24 angstrom (five helical units per step).

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

21BQ | pdb_000021bq