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13rt

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0006249

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13rt
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-0006249
keywords	Macrodomain, ADP-ribose, SARS-CoV-2, fragment-based drug discovery, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	21.64 Å
rg_electron	20.83 Å
i0	21773300.00
molecular_weight	36097.0 kDa
excluded_volume	45481 Å³
envelope_volume	52966 Å³
shell_volume	21351 Å³
envelope_diameter	68.9 Å
shell_rg	27.12 Å
envelope_rg	20.91 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/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	67.6 Å
rg_real	21.58 Å
rg_real_error	0.36 Å
i0_real	2.1770e+07
i0_real_error	2.5770e+05
rg_reciprocal	21.59 Å
i0_reciprocal	21770000.0000
total_estimate	0.9037
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	26.2 Å
skewness	0.285
kurtosis	-0.397
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	3357000.0000
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

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	7168

SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFL

Source

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

Entity 2 non-polymer

description	N-{4-[(4,4-dimethyl-2-oxo-1,3-oxazolidin-3-yl)amino]-9H-pyrimido[4,5-b]indol-8-yl}-2,2-difluoroacetamide
formula_weight	390.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	456

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6. Citations (1)

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length_a	88.755 Å
length_b	88.755 Å
length_c	39.554 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	1.020 Å
resolution_low	44.380 Å
r_factor	0.1531
r_work	0.1520
r_free	0.1736

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

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0006249

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