← Back to search

13rk

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004052

Method: X-RAY DIFFRACTION D_max: 67.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	13rk
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-0004052
keywords	Macrodomain, ADP-ribose, SARS-CoV-2, fragment-based drug discovery, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	21.62 Å
rg_electron	20.83 Å
i0	21751900.00
molecular_weight	36097.0 kDa
excluded_volume	45481 Å³
envelope_volume	53011 Å³
shell_volume	21379 Å³
envelope_diameter	68.9 Å
shell_rg	27.03 Å
envelope_rg	20.89 Å
shape_rg	20.82 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/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	67.6 Å
rg_real	21.56 Å
rg_real_error	0.49 Å
i0_real	2.1750e+07
i0_real_error	3.0130e+05
rg_reciprocal	21.58 Å
i0_reciprocal	21750000.0000
total_estimate	0.8215
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.8 Å
skewness	0.281
kurtosis	-0.396
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	3444000.0000
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

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Non-structural protein 3
formula_weight	18178.8 kDa
ec_number	3.4.19.121, 3.4.22.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7212

SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFL

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	(4M)-4-{4-[(2,2-dimethyl-5-oxopyrrolidin-1-yl)amino]-7H-pyrrolo[2,3-d]pyrimidin-6-yl}-1-methyl-1H-pyrazole-5-carbonitrile
formula_weight	350.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	436

▶

6. Citations (1)

▶

length_a	88.763 Å
length_b	88.763 Å
length_c	39.705 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43
int_tables_number	78
crystal_system	—

resolution	1.030 Å
resolution_low	39.700 Å
r_factor	0.1655
r_work	0.1644
r_free	0.1856

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

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004052

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction