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9s0m

Crystal structure of SARS-CoV-2 NSP14 in complex with compound 1

Method: X-RAY DIFFRACTION D_max: 100.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s0m
deposition_date	2025-07-16
title	Crystal structure of SARS-CoV-2 NSP14 in complex with compound 1
keywords	NSP14, SARS-CoV-2 NSP14, 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	32.34 Å
rg_electron	31.60 Å
i0	305485000.00
molecular_weight	94115.0 kDa
excluded_volume	91253 Å³
envelope_volume	164760 Å³
shell_volume	42487 Å³
envelope_diameter	104.3 Å
shell_rg	39.43 Å
envelope_rg	31.31 Å
shape_rg	31.58 Å
total_rg	32.12 Å
total_atoms	7075
n_residues	897
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	100.3 Å
rg_real	32.16 Å
rg_real_error	0.61 Å
i0_real	3.0550e+08
i0_real_error	4.9670e+06
rg_reciprocal	32.24 Å
i0_reciprocal	305500000.0000
total_estimate	0.9087
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	43.0 Å
skewness	0.095
kurtosis	-0.630
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	29610000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.964

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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	59544.2 kDa
ec_number	2.1.1.56,3.1.13.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7094

AENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKTEGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFAVAGCHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIPLMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCLCDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTFTR

Source

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

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	7

Entity 3 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	(2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-(1,3-benzothiazol-2-ylsulfanylmethyl)oxolane-3,4-diol
formula_weight	416.5 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	19

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6. Citations (1)

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length_a	67.587 Å
length_b	101.864 Å
length_c	91.018 Å
angle_alpha	90.00 °
angle_beta	108.86 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.850 Å
resolution_low	63.960 Å
r_factor	0.2322
r_work	0.2310
r_free	0.2830

fit	/app/data/saxs_computation/s0/9s0m/9s0m.fit
pddf	/app/data/pr_computation/s0/9s0m/9s0m.pr.out
profile	/app/data/saxs_computation/s0/9s0m/9s0m.dat