PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004054

entry_id	13rl
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-0004054
keywords	Macrodomain, ADP-ribose, SARS-CoV-2, fragment-based drug discovery, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

rg_guinier	21.64 Å
rg_electron	20.84 Å
i0	21805400.00
molecular_weight	36097.0 kDa
excluded_volume	45481 ų
envelope_volume	53023 ų
shell_volume	21378 ų
envelope_diameter	69.0 Å
shell_rg	27.09 Å
envelope_rg	20.90 Å
shape_rg	20.83 Å
total_rg	21.71 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	21.59 Å
rg_real_error	0.39 Å
i0_real	2.1810e+07
i0_real_error	2.8570e+05
rg_reciprocal	21.60 Å
i0_reciprocal	21810000.0000
total_estimate	0.9038
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.284
kurtosis	-0.401
angular_range	— – 0.3650 Å−1
current_alpha	0.0000
highest_alpha	3398000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.981

Unit Cell

length_a	88.850 Å
length_b	88.850 Å
length_c	39.563 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	1.020 Å
resolution_low	44.420 Å
r_factor	0.1440
r_work	0.1431
r_free	0.1606

Diffraction

temperature

100.0 K

Files (7)

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

Curves (3)

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