PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004100

entry_id	13rm
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-0004100
keywords	Macrodomain, ADP-ribose, SARS-CoV-2, fragment-based drug discovery, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

rg_guinier	21.62 Å
rg_electron	20.82 Å
i0	21821500.00
molecular_weight	36097.0 kDa
excluded_volume	45481 ų
envelope_volume	52922 ų
shell_volume	21353 ų
envelope_diameter	68.9 Å
shell_rg	27.06 Å
envelope_rg	20.88 Å
shape_rg	20.81 Å
total_rg	21.69 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	68.1 Å
rg_real	21.57 Å
rg_real_error	0.51 Å
i0_real	2.1820e+07
i0_real_error	3.1220e+05
rg_reciprocal	21.58 Å
i0_reciprocal	21820000.0000
total_estimate	0.8214
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.0 Å
skewness	0.282
kurtosis	-0.396
angular_range	— – 0.3700 Å−1
current_alpha	0.0000
highest_alpha	3417000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

Unit Cell

length_a	88.830 Å
length_b	88.830 Å
length_c	39.420 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	1.010 Å
resolution_low	39.730 Å
r_factor	0.1362
r_work	0.1356
r_free	0.1493

Diffraction

temperature

100.0 K

Files (7)

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

Curves (3)

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