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9r6h

Crystal Structure of the M18BP1 SANTA domain as a EGFP-SANTA-nanobody fusion

Method: X-RAY DIFFRACTION D_max: 140.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r6h
deposition_date	2025-05-12
title	Crystal Structure of the M18BP1 SANTA domain as a EGFP-SANTA-nanobody fusion
keywords	centromere binding, mitotic kinetochores, CENP-A loading, Mis18 complex, CELL CYCLE; CELL CYCLE
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	41.36 Å
rg_electron	41.65 Å
i0	173398000.00
molecular_weight	106630.0 kDa
excluded_volume	133330 Å³
envelope_volume	186080 Å³
shell_volume	40065 Å³
envelope_diameter	143.2 Å
shell_rg	42.26 Å
envelope_rg	41.46 Å
shape_rg	41.61 Å
total_rg	41.81 Å
total_atoms	7507
n_residues	917
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	140.2 Å
rg_real	41.79 Å
rg_real_error	1.58 Å
i0_real	1.7340e+08
i0_real_error	3.6610e+06
rg_reciprocal	41.37 Å
i0_reciprocal	173300000.0000
total_estimate	0.7639
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.2 Å
skewness	0.512
kurtosis	-0.608
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	15910000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.594; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.674; Smooth: 0.469

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Genome polyprotein,Mis18-binding protein 1,Chains: A
formula_weight	55381.4 kDa
ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7601

MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLXVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKASTVTNGLKKNQVVQLQEWMIKSINNNTAICVEGKLIDVTNIYWHSNVIIERIEHNKLRTISGNVYILKGMIDQISMKEAGYPNYLIRKFMFGFPENWKEHIDNFLEQLRAGEKNREKTKQLEGTAQVQLVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSAGDRSSYEDSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVSSKGGHHHHHH

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	11

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	94

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6. Citations (1)

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length_a	143.200 Å
length_b	120.280 Å
length_c	77.360 Å
angle_alpha	90.00 °
angle_beta	121.28 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.420 Å
resolution_low	45.040 Å
r_factor	0.2307
r_work	0.2290
r_free	0.2618

fit	/app/data/saxs_computation/r6/9r6h/9r6h.fit
pddf	/app/data/pr_computation/r6/9r6h/9r6h.pr.out
profile	/app/data/saxs_computation/r6/9r6h/9r6h.dat

Crystal Structure of the M18BP1 SANTA domain as a EGFP-SANTA-nanobody fusion

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