9FM2 | pdb_00009fm2

Cryo-EM structure of Influenza B/Washington/02/2019 virus neuraminidase in complex with single-domain antibody hVHH-525.

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	62.647
r_long_range_B_other	62.646
r_scangle_other	46.368
r_mcangle_it	45.69
r_mcangle_other	45.688
r_scbond_it	30.001
r_scbond_other	29.998
r_mcbond_it	29.28
r_mcbond_other	29.267
r_dihedral_angle_3_deg	14.57
r_dihedral_angle_1_deg	5.792
r_dihedral_angle_2_deg	2.717
r_angle_refined_deg	1.352
r_angle_other_deg	0.476
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_gen_planes_other	0.001
r_bond_other_d
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Sample
Complex between Influenza B/Washington/02/2019 virus neuraminidase (tetramer) and one copy of single-domain antibody hVHH-525

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

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	158674
Reported Resolution (Å)	3.6
Resolution Method	FSC 0.143 CUT-OFF
Other Details	Compositional heterogeneity of the sample necessitated the use of a 3D processing strategy combining symmetry expansion, focused 3D classification without alignment, signal subtraction and localized refinement. The final particle set consists of 158674 symmetry expanded and signal subtracted particles.
Refinement Type
Symmetry Type	POINT

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

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	60

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL CRYO ARM 300
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
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
PARTICLE SELECTION	crYOLO
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC	4.2
INITIAL EULER ASSIGNMENT	cryoSPARC	4.2
FINAL EULER ASSIGNMENT	cryoSPARC	4.2
CLASSIFICATION	cryoSPARC	4.2
RECONSTRUCTION	cryoSPARC	4.2

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		697697