Crystal structure of HIV Apex fab Q9M-023

entry_id	9pyn
deposition_date	2025-08-07
last_revision	2026-05-13
title	Crystal structure of HIV Apex fab Q9M-023
keywords	HIV, Apex targeting neutralizing antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

rg_guinier	26.07 Å
rg_electron	25.09 Å
i0	38678900.00
molecular_weight	47501.0 kDa
excluded_volume	59136 ų
envelope_volume	74741 ų
shell_volume	25107 ų
envelope_diameter	91.4 Å
shell_rg	32.11 Å
envelope_rg	24.92 Å
shape_rg	25.09 Å
total_rg	25.89 Å
total_atoms	3347
n_residues	422
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	26.09 Å
rg_real_error	0.85 Å
i0_real	3.8680e+07
i0_real_error	5.7430e+05
rg_reciprocal	26.09 Å
i0_reciprocal	38680000.0000
total_estimate	0.8835
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.3 Å
skewness	0.333
kurtosis	-0.390
angular_range	— – 0.3050 Å−1
current_alpha	0.0000
highest_alpha	7157000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.996

Unit Cell

length_a	61.727 Å
length_b	73.054 Å
length_c	132.529 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	orthorhombic

Refinement

resolution	2.340 Å
resolution_low	33.130 Å
r_factor	0.2337
r_work	0.2317
r_free	0.2735

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/py/9pyn/pr_distribution.json
• pr_output /app/data/pr_computation/py/9pyn/9pyn.pr.out
• pr_plot /app/data/visualization/pr_computation/py/9pyn/9pyn_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/py/9pyn/9pyn.dat
• saxs_fit /app/data/saxs_computation/py/9pyn/9pyn.fit
• saxs_log /app/data/saxs_computation/py/9pyn/9pyn.log
• saxs_plot /app/data/visualization/saxs_computation/py/9pyn/9pyn_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/py/9pyn/9pyn.fit
pddf	/app/data/pr_computation/py/9pyn/9pyn.pr.out
profile	/app/data/saxs_computation/py/9pyn/9pyn.dat