;Structure of the Porcine deltacoronavirus (PDCoV) receptor-binding domain bound to the RBD minibinder 11, the PD3 Fab, and the Kappa light chain nanobody (local refinement) ;

entry_id	11zv
deposition_date	2026-03-21
title	;Structure of the Porcine deltacoronavirus (PDCoV) receptor-binding domain bound to the RBD minibinder 11, the PD3 Fab, and the Kappa light chain nanobody (local refinement) ;
keywords	;porcine deltacoronavirus, minibinder, protein design, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, VIRAL PROTEIN ;; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

rg_guinier	22.06 Å
rg_electron	21.38 Å
i0	13200500.00
molecular_weight	27893.0 kDa
excluded_volume	35161 ų
envelope_volume	42291 ų
shell_volume	17543 ų
envelope_diameter	70.8 Å
shell_rg	26.81 Å
envelope_rg	21.54 Å
shape_rg	21.38 Å
total_rg	22.18 Å
total_atoms	1956
n_residues	240
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	70.1 Å
rg_real	22.14 Å
rg_real_error	0.45 Å
i0_real	1.3200e+07
i0_real_error	1.8860e+05
rg_reciprocal	22.13 Å
i0_reciprocal	13200000.0000
total_estimate	0.8919
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.0 Å
skewness	0.385
kurtosis	-0.503
angular_range	— – 0.3600 Å−1
current_alpha	0.0000
highest_alpha	2807000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.989

Unit Cell

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

Symmetry

space_group	P 1
int_tables_number	1
crystal_system	—

Refinement

resolution	2.840 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

EM 3D

resolution	2.84 Å
resolution_method	—
num_particles	512440

Files (7)

• pr_distribution /app/data/pr_computation/1z/11zv/pr_distribution.json
• pr_output /app/data/pr_computation/1z/11zv/11zv.pr.out
• pr_plot /app/data/visualization/pr_computation/1z/11zv/11zv_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/1z/11zv/11zv.dat
• saxs_fit /app/data/saxs_computation/1z/11zv/11zv.fit
• saxs_log /app/data/saxs_computation/1z/11zv/11zv.log
• saxs_plot /app/data/visualization/saxs_computation/1z/11zv/11zv_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/1z/11zv/11zv.fit
pddf	/app/data/pr_computation/1z/11zv/11zv.pr.out
profile	/app/data/saxs_computation/1z/11zv/11zv.dat