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13ym

PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z19727416

Method: X-RAY DIFFRACTION D_max: 70.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13ym
deposition_date	2026-03-06
last_revision	2026-03-18
title	PanDDA analysis group deposition -- Crystal Structure of Enterovirus D68 3Dpol in complex with Z19727416
keywords	SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, RNA-dependent RNA polymerase, TRANSFERASE; TRANSFERASE
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	24.19 Å
rg_electron	23.06 Å
i0	43981600.00
molecular_weight	53190.0 kDa
excluded_volume	67363 Å³
envelope_volume	82980 Å³
shell_volume	29257 Å³
envelope_diameter	73.9 Å
shell_rg	30.73 Å
envelope_rg	22.87 Å
shape_rg	23.05 Å
total_rg	24.03 Å
total_atoms	3739
n_residues	457
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	70.8 Å
rg_real	23.97 Å
rg_real_error	0.26 Å
i0_real	4.3980e+07
i0_real_error	5.1160e+05
rg_reciprocal	24.03 Å
i0_reciprocal	43980000.0000
total_estimate	0.9118
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	69.7 Å
skewness	0.007
kurtosis	-0.589
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	12440000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	3Dpol RNA Dependent RNA Polymerase
formula_weight	52958.3 kDa
ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4061

GEIVSNEKSGVCINAPAKTKLQPSVFHQVFEGSKEPAVLNSKDPRLKTDFEEAIFSKYTGNKIMLMDEYMEEAVDHYVGCLEPLDISVDPIPLESAMYGMDGLEALDLTTSAGFPYLLQGKKKRDIFNRHTRDTTEMTKMLEKYGVDLPFVTFVKDELRSKEKVEKGKSRLIEASSLNDSVAMRVAFGNLYATFHSNPGTATGSAVGCDPDIFWSKIPILLDGEIFAFDYTGYDASLSPVWFACLKKVLIKLGYTHQTSFIDYLCHSVHLYKDRKYIVNGGMPSGSSGTSIFNTMINNIIIRTLLIRVYKGIDLDQFKMIAYGDDVIASYPHKIDPALLAEAGKHYGLVMTPADKGTSFVDTNWENVTFLKRYFRADDQYPFLIHPVMPMKEIHESIRWTKDPRNTQDHVRSLCYLAWHNGEEAYNEFCRKIRSVPVGRALTLPAYSSLRRKWLDSFGSSGHHHHHH

Source

organism	enterovirus D68
ncbi_taxonomy_id	42789
host_organism	Escherichia coli

Entity 2 non-polymer

description	ISOPROPYL ALCOHOL
formula_weight	60.1 kDa
src_method	syn
entity_count	15

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	(2R)-2-(4-chlorophenoxy)propanamide
formula_weight	199.6 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	322

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6. Citations (1)

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length_a	55.586 Å
length_b	83.808 Å
length_c	58.937 Å
angle_alpha	90.00 °
angle_beta	108.51 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.340 Å
resolution_low	55.890 Å
r_factor	0.1838
r_work	0.1826
r_free	0.2049

fit	/app/data/saxs_computation/3y/13ym/13ym.fit
pddf	/app/data/pr_computation/3y/13ym/13ym.pr.out
profile	/app/data/saxs_computation/3y/13ym/13ym.dat