9PSL | pdb_00009psl

Co-crystal structure of BAF60A (SMARCD1) in complex with PU.1 peptide

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Alphafold2 model of BAF60A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	0.1M Sodium citrate pH 6.48, 1.97M Ammonium sulfate, 2% v/v PEGMME550, 0.01M Taurine, 10 mM Ethylenediaminetetraacetic disodium salt dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.75	α = 90
b = 131.85	β = 93.44
c = 75.36	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 6M		2023-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.39	49.63	99.7	0.14	0.151	0.057	10.6	7		46704

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.39	2.47		99.3	0.907	0.977	0.362		7.1

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	2.39	49.63	44356	2341	99.6	0.22722	0.22432	0.2307	0.28356	0.2852	RANDOM	60.204

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]
-0.78		0.21	0.57		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.26
r_long_range_B_refined	6.04
r_long_range_B_other	6
r_dihedral_angle_1_deg	5.86
r_scangle_other	3.778
r_mcangle_it	3.698
r_mcangle_other	3.698
r_dihedral_angle_2_deg	2.994
r_mcbond_it	2.209
r_mcbond_other	2.209
r_scbond_it	2.209
r_scbond_other	2.208
r_angle_refined_deg	0.837
r_angle_other_deg	0.313
r_chiral_restr	0.04
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	7820
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	48

Software

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