PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004683

entry_id	13rq
deposition_date	2025-10-09
last_revision	2026-01-28
title	PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004683
keywords	Macrodomain, ADP-ribose, SARS-CoV-2, fragment-based drug discovery, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

rg_guinier	21.63 Å
rg_electron	20.83 Å
i0	21789400.00
molecular_weight	36097.0 kDa
excluded_volume	45481 ų
envelope_volume	52918 ų
shell_volume	21347 ų
envelope_diameter	68.9 Å
shell_rg	27.10 Å
envelope_rg	20.89 Å
shape_rg	20.82 Å
total_rg	21.70 Å
total_atoms	5107
n_residues	336
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	67.6 Å
rg_real	21.57 Å
rg_real_error	0.33 Å
i0_real	2.1790e+07
i0_real_error	2.6340e+05
rg_reciprocal	21.58 Å
i0_reciprocal	21790000.0000
total_estimate	0.9018
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.2 Å
skewness	0.285
kurtosis	-0.400
angular_range	— – 0.3650 Å−1
current_alpha	0.0000
highest_alpha	3401000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.954

Unit Cell

length_a	88.724 Å
length_b	88.724 Å
length_c	39.642 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

Symmetry

space_group	P 43
int_tables_number	78
crystal_system	—

Refinement

resolution	0.990 Å
resolution_low	44.360 Å
r_factor	0.1468
r_work	0.1461
r_free	0.1610

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/3r/13rq/pr_distribution.json
• pr_output /app/data/pr_computation/3r/13rq/13rq.pr.out
• pr_plot /app/data/visualization/pr_computation/3r/13rq/13rq_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/3r/13rq/13rq.dat
• saxs_fit /app/data/saxs_computation/3r/13rq/13rq.fit
• saxs_log /app/data/saxs_computation/3r/13rq/13rq.log
• saxs_plot /app/data/visualization/saxs_computation/3r/13rq/13rq_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/3r/13rq/13rq.fit
pddf	/app/data/pr_computation/3r/13rq/13rq.pr.out
profile	/app/data/saxs_computation/3r/13rq/13rq.dat