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9qra

SARS-CoV-2 nsp14 with 1-(4-methylphenyl)-2-(2-methylsulfanyl-4,5-dihydroimidazol-1-yl)ethanone

Method: X-RAY DIFFRACTION D_max: 86.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qra
deposition_date	2025-04-03
last_revision	2026-04-29
title	SARS-CoV-2 nsp14 with 1-(4-methylphenyl)-2-(2-methylsulfanyl-4,5-dihydroimidazol-1-yl)ethanone
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	26.93 Å
rg_electron	26.55 Å
i0	79462600.00
molecular_weight	47131.0 kDa
excluded_volume	45756 Å³
envelope_volume	77381 Å³
shell_volume	25417 Å³
envelope_diameter	89.8 Å
shell_rg	32.70 Å
envelope_rg	26.64 Å
shape_rg	26.53 Å
total_rg	27.09 Å
total_atoms	3537
n_residues	446
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	86.9 Å
rg_real	27.08 Å
rg_real_error	0.67 Å
i0_real	7.9460e+07
i0_real_error	1.1690e+06
rg_reciprocal	27.04 Å
i0_reciprocal	79460000.0000
total_estimate	0.8705
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.5 Å
skewness	0.428
kurtosis	-0.533
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	7205000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.893

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	3702

TMLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTRLQ

Source

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

Entity 2 non-polymer

description	1-(4-methylphenyl)-2-(2-methylsulfanylimidazol-1-yl)ethanone
formula_weight	246.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	152

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6. Citations (1)

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length_a	68.115 Å
length_b	68.392 Å
length_c	138.667 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	—

resolution	2.290 Å
resolution_low	48.690 Å
r_factor	0.1934
r_work	0.1906
r_free	0.2495

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