Experiment: 9YBR

Binding Sites in the ARID1B DNA Binding Domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CXY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	1.5 M sodium citrate, pH 6.5, 0.033% w/v 4-nitrobenzoic acid, 0.033% w/v 5-sulfosalicylic acid dihydrate, 0.033% w/v naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.002 M HEPES sodium, pH 6.8

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.835	α = 90
b = 68.835	β = 90
c = 46.006	γ = 120

Symmetry
Space Group	P 65

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		2023-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.953725	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.45	36.42	100	0.09	0.02	0.999	18.6	20.35		22134			17.96

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.5	100		1.503	0.814	2.1	19.11

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.45	34.42	1.35	22115	1983	99.91	0.1515	0.1506	0.1496	0.161	0.1597	25.19

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.8364
f_angle_d	1.0117
f_chiral_restr	0.0723
f_plane_restr	0.0095
f_bond_d	0.0085

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	892
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	4

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
XSCALE	data scaling
PHASER	phasing