4Z1S

Crystal structure of the first bromodomain of human BRD4 with benzotriazolo-diazepine scaffold

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M potassium sodium tartrate and 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.376	α = 82.6
b = 39.508	β = 75.43
c = 57.358	γ = 90

Symmetry
Space Group	P 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	CCD	RAYONIX MX-300		2015-01-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9795	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.06	50	91.4	0.055	14.6	2.1		105981

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.06	1.1	77.9		0.34	2.2	1.7	9046

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	Internal model of BRD4-BD1	1.06	50	100690	5291	91.27	0.1871	0.1854	0.2196	RANDOM	14.553

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]
0.52	-0.28	-0.89	-1.26	0.46	0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.333
r_sphericity_free	21.485
r_dihedral_angle_4_deg	17.177
r_dihedral_angle_3_deg	13.755
r_sphericity_bonded	8.203
r_rigid_bond_restr	6.924
r_dihedral_angle_1_deg	5.486
r_angle_refined_deg	2.347
r_mcangle_it	1.628
r_mcbond_it	1.391

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.333
r_sphericity_free	21.485
r_dihedral_angle_4_deg	17.177
r_dihedral_angle_3_deg	13.755
r_sphericity_bonded	8.203
r_rigid_bond_restr	6.924
r_dihedral_angle_1_deg	5.486
r_angle_refined_deg	2.347
r_mcangle_it	1.628
r_mcbond_it	1.391
r_mcbond_other	1.378
r_angle_other_deg	1.068
r_chiral_restr	0.141
r_bond_refined_d	0.028
r_gen_planes_refined	0.014
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2085
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

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.