Crystal structure of HIV Apex neutralizing Fab Q12QBM-007

entry_id	9pz2
deposition_date	2025-08-08
last_revision	2026-05-13
title	Crystal structure of HIV Apex neutralizing Fab Q12QBM-007
keywords	HIV Apex neutralizing antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

rg_guinier	25.95 Å
rg_electron	25.02 Å
i0	39015100.00
molecular_weight	47855.0 kDa
excluded_volume	59604 ų
envelope_volume	74802 ų
shell_volume	25332 ų
envelope_diameter	94.9 Å
shell_rg	31.85 Å
envelope_rg	24.81 Å
shape_rg	25.01 Å
total_rg	25.79 Å
total_atoms	3372
n_residues	427
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	89.4 Å
rg_real	25.95 Å
rg_real_error	0.65 Å
i0_real	3.9020e+07
i0_real_error	5.7630e+05
rg_reciprocal	25.95 Å
i0_reciprocal	39020000.0000
total_estimate	0.8742
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.3 Å
skewness	0.320
kurtosis	-0.358
angular_range	— – 0.3050 Å−1
current_alpha	0.0000
highest_alpha	7274000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.883

Unit Cell

length_a	72.866 Å
length_b	89.150 Å
length_c	89.817 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	1.544 Å
resolution_low	35.136 Å
r_factor	—
r_work	0.1898
r_free	0.2083

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/pz/9pz2/pr_distribution.json
• pr_output /app/data/pr_computation/pz/9pz2/9pz2.pr.out
• pr_plot /app/data/visualization/pr_computation/pz/9pz2/9pz2_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/pz/9pz2/9pz2.dat
• saxs_fit /app/data/saxs_computation/pz/9pz2/9pz2.fit
• saxs_log /app/data/saxs_computation/pz/9pz2/9pz2.log
• saxs_plot /app/data/visualization/saxs_computation/pz/9pz2/9pz2_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/pz/9pz2/9pz2.fit
pddf	/app/data/pr_computation/pz/9pz2/9pz2.pr.out
profile	/app/data/saxs_computation/pz/9pz2/9pz2.dat