Crystal structure of yeast arginine N-methyltransferase 1,HMT1

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

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vkf
deposition_date	2025-06-23
last_revision	2025-07-09
title	Crystal structure of yeast arginine N-methyltransferase 1,HMT1
keywords	homo dimer, Protein arginine N-methyltransferase 1, HMT1, GENE REGULATION., NUCLEAR PROTEIN, GENE REGULATION; GENE REGULATION
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	28.76 Å
rg_electron	27.68 Å
i0	65587200.00
molecular_weight	65764.0 kDa
excluded_volume	83093 Å³
envelope_volume	104430 Å³
shell_volume	31192 Å³
envelope_diameter	95.7 Å
shell_rg	35.41 Å
envelope_rg	27.19 Å
shape_rg	27.67 Å
total_rg	28.53 Å
total_atoms	9102
n_residues	579
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	28.63 Å
rg_real_error	0.74 Å
i0_real	6.5590e+07
i0_real_error	1.0380e+06
rg_reciprocal	28.69 Å
i0_reciprocal	65590000.0000
total_estimate	0.9048
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	43.4 Å
skewness	0.069
kurtosis	-0.685
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	29340000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.941

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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6. Citations (1)

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length_a	84.670 Å
length_b	84.670 Å
length_c	97.720 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31
int_tables_number	144
crystal_system	—

resolution	2.850 Å
resolution_low	34.330 Å
r_factor	0.2349
r_work	0.2349
r_free	0.2837

description	Protein arginine N-methyltransferase 1
formula_weight	37679.6 kDa
ec_number	2.1.1.319
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	9102

Crystal structure of yeast arginine N-methyltransferase 1,HMT1

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
common_name	;brewer's yeast ;
ncbi_taxonomy_id	559292
host_organism	Escherichia coli

fit	/app/data/saxs_computation/vk/9vkf/9vkf.fit
pddf	/app/data/pr_computation/vk/9vkf/9vkf.pr.out
profile	/app/data/saxs_computation/vk/9vkf/9vkf.dat