HRV14 3C in complex with single chain antibody YDF and cloverleafRNA-conformation2 splitRNA

entry_id	9vmd
deposition_date	2025-06-27
title	HRV14 3C in complex with single chain antibody YDF and cloverleafRNA-conformation2 splitRNA
keywords	cloverleafRNA, 3c, complex, RNA BINDING PROTEIN/IMMUNE SYSTEM/RNA, RNA BINDING PROTEIN-IMMUNE SYSTEM-RNA complex; RNA BINDING PROTEIN/IMMUNE SYSTEM/RNA
method	ELECTRON MICROSCOPY

rg_guinier	30.57 Å
rg_electron	29.38 Å
i0	121816000.00
molecular_weight	68985.0 kDa
excluded_volume	78480 ų
envelope_volume	114180 ų
shell_volume	33307 ų
envelope_diameter	106.2 Å
shell_rg	35.50 Å
envelope_rg	28.90 Å
shape_rg	29.29 Å
total_rg	30.09 Å
total_atoms	4743
n_residues	489
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	99.3 Å
rg_real	30.46 Å
rg_real_error	0.69 Å
i0_real	1.2180e+08
i0_real_error	1.5840e+06
rg_reciprocal	30.51 Å
i0_reciprocal	121800000.0000
total_estimate	0.7115
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	38.2 Å
skewness	0.184
kurtosis	-0.384
angular_range	— – 0.2600 Å−1
current_alpha	0.0000
highest_alpha	5128000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 1.000; Smooth: 0.966

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	4.380 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

EM 3D

resolution	4.38 Å
resolution_method	—
num_particles	170015

Files (7)

• pr_distribution /app/data/pr_computation/vm/9vmd/pr_distribution.json
• pr_output /app/data/pr_computation/vm/9vmd/9vmd.pr.out
• pr_plot /app/data/visualization/pr_computation/vm/9vmd/9vmd_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/vm/9vmd/9vmd.dat
• saxs_fit /app/data/saxs_computation/vm/9vmd/9vmd.fit
• saxs_log /app/data/saxs_computation/vm/9vmd/9vmd.log
• saxs_plot /app/data/visualization/saxs_computation/vm/9vmd/9vmd_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/vm/9vmd/9vmd.fit
pddf	/app/data/pr_computation/vm/9vmd/9vmd.pr.out
profile	/app/data/saxs_computation/vm/9vmd/9vmd.dat