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9t2g

Human PRKCBP1 zinc finger MYND-type containing 8 with crystallization epitope mutations N221R:M226H

Method: X-RAY DIFFRACTION D_max: 79.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t2g
deposition_date	2025-10-22
last_revision	2025-11-26
title	Human PRKCBP1 zinc finger MYND-type containing 8 with crystallization epitope mutations N221R:M226H
keywords	crystal epitope, 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	24.48 Å
rg_electron	23.93 Å
i0	22596000.00
molecular_weight	36132.0 kDa
excluded_volume	45203 Å³
envelope_volume	59050 Å³
shell_volume	21385 Å³
envelope_diameter	80.0 Å
shell_rg	29.96 Å
envelope_rg	23.86 Å
shape_rg	23.98 Å
total_rg	24.59 Å
total_atoms	2521
n_residues	308
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	79.6 Å
rg_real	24.58 Å
rg_real_error	0.60 Å
i0_real	2.2600e+07
i0_real_error	3.1200e+05
rg_reciprocal	24.56 Å
i0_reciprocal	22600000.0000
total_estimate	0.8828
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.0 Å
skewness	0.379
kurtosis	-0.541
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	4893000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.883; Smooth: 0.953

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	MYND-type zinc finger-containing chromatin reader ZMYND8
formula_weight	37883.8 kDa
mutation	N221R:M226H
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2878

SMQDGRNDFYCWVCHREGQVLCCELCPRVYHAKCLRLTSEPEGDWFCPECEKITVAECIETQSKAMTMLTIEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKRAKKKHYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIKICEHEMNEIEVCPECYLAACQKRDNWFCEPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRAWVPINNCYLMSKEIPFSVKKTKSIFNSAMQEMEVYVENIRRKFGVFNYSPFRTPYTPNSQYQMLLDPTNPSAGTAKIDKQEKVKLNFDMTAS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	3

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	348

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6. Citations (1)

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length_a	68.802 Å
length_b	71.929 Å
length_c	72.529 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	1.660 Å
resolution_low	49.920 Å
r_factor	0.2388
r_work	0.2372
r_free	0.2690

fit	/app/data/saxs_computation/t2/9t2g/9t2g.fit
pddf	/app/data/pr_computation/t2/9t2g/9t2g.pr.out
profile	/app/data/saxs_computation/t2/9t2g/9t2g.dat

Human PRKCBP1 zinc finger MYND-type containing 8 with crystallization epitope mutations N221R:M226H

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