4XY9

Crystal Structure of the first bromodomain of human BRD4 in complex with a 2-amine-9H-purine ligand

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.20M NaNO3, 20.0% PEG 3350, 10.0% EtGly

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.915	α = 90
b = 44.229	β = 90
c = 79.584	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	CCD	APEX II CCD		2014-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	1.83	44.23	100	0.064	0.064	16.98	5.15		12065

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.87	99.8		0.202	2.29	3.61

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.83	39.79	11421	601	99.97	0.1598	0.1572	0.2061	RANDOM	18.723

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]
0.5			-0.08		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.302
r_dihedral_angle_4_deg	24.438
r_dihedral_angle_3_deg	13.467
r_sphericity_bonded	10.521
r_dihedral_angle_1_deg	5.566
r_mcangle_it	3.832
r_mcbond_it	2.553
r_mcbond_other	2.509
r_angle_refined_deg	1.66
r_angle_other_deg	0.895

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.302
r_dihedral_angle_4_deg	24.438
r_dihedral_angle_3_deg	13.467
r_sphericity_bonded	10.521
r_dihedral_angle_1_deg	5.566
r_mcangle_it	3.832
r_mcbond_it	2.553
r_mcbond_other	2.509
r_angle_refined_deg	1.66
r_angle_other_deg	0.895
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1047
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	23

Software

Software
Software Name	Purpose
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.