Crystal structure of 5B3 Fab in complex with PvRipr EGF7-8

entry_id	9yio
deposition_date	2025-10-02
title	Crystal structure of 5B3 Fab in complex with PvRipr EGF7-8
keywords	Plasmodium vivax, invasion, antibody-antigen complex, CELL INVASION; CELL INVASION
method	X-RAY DIFFRACTION

rg_guinier	28.45 Å
rg_electron	28.16 Å
i0	55144200.00
molecular_weight	56631.0 kDa
excluded_volume	70229 ų
envelope_volume	90335 ų
shell_volume	28200 ų
envelope_diameter	102.8 Å
shell_rg	33.69 Å
envelope_rg	28.24 Å
shape_rg	28.07 Å
total_rg	28.98 Å
total_atoms	3970
n_residues	506
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	97.5 Å
rg_real	28.64 Å
rg_real_error	1.24 Å
i0_real	5.5140e+07
i0_real_error	8.9980e+05
rg_reciprocal	28.58 Å
i0_reciprocal	55140000.0000
total_estimate	0.8667
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.6 Å
skewness	0.497
kurtosis	-0.175
angular_range	— – 0.2800 Å−1
current_alpha	0.0000
highest_alpha	7298000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.952

Unit Cell

length_a	80.270 Å
length_b	81.746 Å
length_c	92.149 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

Symmetry

space_group	P 21 21 2
int_tables_number	18
crystal_system	orthorhombic

Refinement

resolution	2.080 Å
resolution_low	48.640 Å
r_factor	0.2058
r_work	0.2041
r_free	0.2354

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/yi/9yio/pr_distribution.json
• pr_output /app/data/pr_computation/yi/9yio/9yio.pr.out
• pr_plot /app/data/visualization/pr_computation/yi/9yio/9yio_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/yi/9yio/9yio.dat
• saxs_fit /app/data/saxs_computation/yi/9yio/9yio.fit
• saxs_log /app/data/saxs_computation/yi/9yio/9yio.log
• saxs_plot /app/data/visualization/saxs_computation/yi/9yio/9yio_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/yi/9yio/9yio.fit
pddf	/app/data/pr_computation/yi/9yio/9yio.pr.out
profile	/app/data/saxs_computation/yi/9yio/9yio.dat