9PSJ | pdb_00009psj

Crystal structure of BAF60A (SMARCD1) apo containing partial coiled coil and the YEATS-like domain with topologically-linked SWIB

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Alphafold2 model was used as an input in MrBUMP automated molecular replacement

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	20% w/v PEG3350, 0.2 M NH4NO3

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.555	α = 90
b = 69.346	β = 120.47
c = 77.958	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2025-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.98011	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.09	35.6	98.8	0.994	10.7	3.7		22251

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.14			0.858

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.09	35.58	21060	1186	98.47	0.21389	0.21086	0.2166	0.2658	0.266	RANDOM	49.013

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
4.13		-3.35	2.51		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.265
r_dihedral_angle_3_deg	17.633
r_dihedral_angle_4_deg	13.436
r_long_range_B_refined	9.22
r_long_range_B_other	9.202
r_dihedral_angle_1_deg	7.088
r_scangle_other	6.932
r_mcangle_other	5.684
r_mcangle_it	5.68
r_scbond_it	4.704
r_scbond_other	4.703
r_mcbond_it	4.047
r_mcbond_other	4.034
r_angle_refined_deg	1.498
r_angle_other_deg	1.242
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2007
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling