Crystal structure of HIV Apex targeting neutralizing antibody Q12BBM-069

entry_id	9pz3
deposition_date	2025-08-08
last_revision	2026-05-13
title	Crystal structure of HIV Apex targeting neutralizing antibody Q12BBM-069
keywords	HIV, Apex neutralizing antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

rg_guinier	25.47 Å
rg_electron	24.54 Å
i0	38528700.00
molecular_weight	47574.0 kDa
excluded_volume	59290 ų
envelope_volume	73380 ų
shell_volume	25297 ų
envelope_diameter	91.9 Å
shell_rg	31.27 Å
envelope_rg	24.54 Å
shape_rg	24.54 Å
total_rg	25.31 Å
total_atoms	3355
n_residues	421
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	89.5 Å
rg_real	25.48 Å
rg_real_error	0.67 Å
i0_real	3.8530e+07
i0_real_error	5.8580e+05
rg_reciprocal	25.48 Å
i0_reciprocal	38530000.0000
total_estimate	0.8734
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.9 Å
skewness	0.346
kurtosis	-0.305
angular_range	— – 0.3100 Å−1
current_alpha	0.0000
highest_alpha	7715000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.998

Unit Cell

length_a	56.419 Å
length_b	72.502 Å
length_c	175.215 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

Symmetry

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

Refinement

resolution	1.790 Å
resolution_low	33.497 Å
r_factor	0.2125
r_work	0.2111
r_free	0.2401

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/pz/9pz3/pr_distribution.json
• pr_output /app/data/pr_computation/pz/9pz3/9pz3.pr.out
• pr_plot /app/data/visualization/pr_computation/pz/9pz3/9pz3_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/pz/9pz3/9pz3.dat
• saxs_fit /app/data/saxs_computation/pz/9pz3/9pz3.fit
• saxs_log /app/data/saxs_computation/pz/9pz3/9pz3.log
• saxs_plot /app/data/visualization/saxs_computation/pz/9pz3/9pz3_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/pz/9pz3/9pz3.fit
pddf	/app/data/pr_computation/pz/9pz3/9pz3.pr.out
profile	/app/data/saxs_computation/pz/9pz3/9pz3.dat