6G0O

Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated ATRX peptide (K1030ac/K1033ac)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	20.0 % PEG 6K 10.0 % EtGly 0.1 M HEPES pH 7.0 0.2 M LiCl

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.864	α = 90
b = 52.797	β = 90
c = 53.317	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	100	PIXEL	DECTRIS PILATUS 6M-F		2016-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.4	53.317	99.2	0.073	0.073	0.08	0.031	17.9	6.4		27568

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.48	98		0.388	0.388	0.425	0.172	1.8	6

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	THROUGHOUT	Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C, 3DWY	1.4	37.52	26339	1186	98.96	0.135	0.1336	0.1661	RANDOM	16.198

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]
-0.1			0.87		-0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.794
r_sphericity_free	25.458
r_dihedral_angle_4_deg	20.214
r_dihedral_angle_3_deg	10.917
r_sphericity_bonded	9.065
r_dihedral_angle_1_deg	6.23
r_rigid_bond_restr	3.596
r_angle_refined_deg	1.723
r_angle_other_deg	0.945
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.794
r_sphericity_free	25.458
r_dihedral_angle_4_deg	20.214
r_dihedral_angle_3_deg	10.917
r_sphericity_bonded	9.065
r_dihedral_angle_1_deg	6.23
r_rigid_bond_restr	3.596
r_angle_refined_deg	1.723
r_angle_other_deg	0.945
r_chiral_restr	0.107
r_bond_refined_d	0.014
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1141
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	12

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.