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9t3m

Crystal Structure of 11 bound to the PH domain of Btk

Method: X-RAY DIFFRACTION D_max: 98.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t3m
deposition_date	2025-10-28
title	Crystal Structure of 11 bound to the PH domain of Btk
keywords	Fragment based drug discovery, ph domain, Hydrolase; HYDROLASE
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	31.09 Å
rg_electron	30.25 Å
i0	159222000.00
molecular_weight	68098.0 kDa
excluded_volume	66438 Å³
envelope_volume	121210 Å³
shell_volume	33234 Å³
envelope_diameter	99.8 Å
shell_rg	37.35 Å
envelope_rg	29.79 Å
shape_rg	30.14 Å
total_rg	30.94 Å
total_atoms	5161
n_residues	616
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	98.8 Å
rg_real	31.02 Å
rg_real_error	0.80 Å
i0_real	1.5920e+08
i0_real_error	2.6980e+06
rg_reciprocal	31.05 Å
i0_reciprocal	159200000.0000
total_estimate	0.9006
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	44.6 Å
skewness	0.181
kurtosis	-0.595
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	35260000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.921

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Tyrosine-protein kinase BTK
formula_weight	19966.9 kDa
ec_number	2.7.10.2
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	5480

AAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPSFWIDGQYLCCSQTAKNAMGCQILEN

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	(6~{S})-6-(2-methoxyphenyl)-4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid
formula_weight	272.3 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	309

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6. Citations (1)

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length_a	68.593 Å
length_b	67.071 Å
length_c	79.926 Å
angle_alpha	90.00 °
angle_beta	99.77 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	67.600 Å
r_factor	0.2480
r_work	0.2453
r_free	0.2977

fit	/app/data/saxs_computation/t3/9t3m/9t3m.fit
pddf	/app/data/pr_computation/t3/9t3m/9t3m.pr.out
profile	/app/data/saxs_computation/t3/9t3m/9t3m.dat