7S4E

Crystal Structure of ligand ACBi1 in complex with bromodomain of human Smarca2 and pVHL:ElonginC:ElonginB complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HAX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.85	277.15	0.1 M HEPES, pH 7.85, 13% PEG 3350, 0.2 M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.14	α = 90
b = 116.57	β = 90
c = 122.32	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77.15	PIXEL	DECTRIS EIGER X 16M		2021-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97932	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.25	37.92	99.9	0.149	0.16	0.058	0.998	8	7.4		55100

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31	99.9		2.602	2.797	1.017	0.317		7.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6HAX	2.25	37.92	52206	2828	99.92	0.221	0.219	0.2587	RANDOM	61.139

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]
-3.16			-0.21		3.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.404
r_dihedral_angle_4_deg	20.826
r_dihedral_angle_3_deg	15.636
r_dihedral_angle_1_deg	7.601
r_angle_refined_deg	1.519
r_angle_other_deg	1.185
r_chiral_restr	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.404
r_dihedral_angle_4_deg	20.826
r_dihedral_angle_3_deg	15.636
r_dihedral_angle_1_deg	7.601
r_angle_refined_deg	1.519
r_angle_other_deg	1.185
r_chiral_restr	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7356
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	196

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.