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9qrc

SARS-CoV-2 nsp14 with 6-methyl-2-[(4-methylphenyl)methyl]pyridazin-3-one

Method: X-RAY DIFFRACTION D_max: 88.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qrc
deposition_date	2025-04-03
last_revision	2026-04-15
title	SARS-CoV-2 nsp14 with 6-methyl-2-[(4-methylphenyl)methyl]pyridazin-3-one
keywords	SARS-CoV-2, nsp14, Fragment screening, 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	26.97 Å
rg_electron	26.62 Å
i0	78525600.00
molecular_weight	46974.0 kDa
excluded_volume	45662 Å³
envelope_volume	78023 Å³
shell_volume	25588 Å³
envelope_diameter	90.1 Å
shell_rg	32.80 Å
envelope_rg	26.68 Å
shape_rg	26.61 Å
total_rg	27.15 Å
total_atoms	3529
n_residues	445
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	88.3 Å
rg_real	27.13 Å
rg_real_error	0.64 Å
i0_real	7.8530e+07
i0_real_error	1.0720e+06
rg_reciprocal	27.08 Å
i0_reciprocal	78520000.0000
total_estimate	0.8615
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.9 Å
skewness	0.436
kurtosis	-0.523
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	7489000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.835; Smooth: 0.885

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Guanine-N7 methyltransferase nsp14
formula_weight	59548.2 kDa
ec_number	2.1.1.56,3.1.13.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3606

TMLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Escherichia coli

Entity 2 non-polymer

description	6-methyl-2-[(4-methylphenyl)methyl]pyridazin-3-one
formula_weight	214.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	64

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6. Citations (1)

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length_a	67.992 Å
length_b	68.431 Å
length_c	139.284 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.400 Å
resolution_low	61.100 Å
r_factor	0.1964
r_work	0.1940
r_free	0.2395

fit	/app/data/saxs_computation/qr/9qrc/9qrc.fit
pddf	/app/data/pr_computation/qr/9qrc/9qrc.pr.out
profile	/app/data/saxs_computation/qr/9qrc/9qrc.dat