8QSY | pdb_00008qsy

Portal capsid interface of full Haloferax tailed virus 1.

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.358
r_dihedral_angle_4_deg	18.984
r_dihedral_angle_3_deg	12.989
r_lrange_it	9.291
r_dihedral_angle_1_deg	7.611
r_scangle_it	4.681
r_mcangle_it	3.496
r_scbond_it	2.754
r_mcbond_it	1.994
r_angle_refined_deg	1.581
r_nbtor_refined	0.289
r_nbd_refined	0.198
r_chiral_restr	0.104
r_xyhbond_nbd_refined	0.077
r_metal_ion_refined	0.059
r_gen_planes_refined	0.009
r_bond_refined_d	0.005

Sample
Haloferax tailed virus 1

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	157388
Reported Resolution (Å)	2.68
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space	RECIPROCAL
Refinement Protocol	AB INITIO MODEL
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	TFS FALCON 4i (4k x 4k)	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	50	54.6

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	TFS KRIOS
Minimum Defocus (nm)	800
Maximum Defocus (nm)	2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
IMAGE ACQUISITION	EPU	5
CTF CORRECTION	RELION	4.0-beta
MODEL FITTING	Coot
MODEL FITTING	UCSF ChimeraX
MODEL FITTING	ISOLDE
MODEL REFINEMENT	REFMAC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION