7JKY

Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with YF3-126

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	0.2M LiSO4, 0.1M Tris-HCl pH 8.5, 16-20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.196	α = 90
b = 42.303	β = 90
c = 91.235	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	RAYONIX MX-300		2019-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.16	20.74	99.8	0.045	0.049	18.4	6.9		52027

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.16	1.18	96.1		0.323	0.357	4.2	5.4

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	THROUGHOUT	3MXF	1.16	20.74	49418	2541	99.76	0.1622	0.1615	0.1758	RANDOM	10.911

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]
0.66			-0.16		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.359
r_dihedral_angle_4_deg	22.549
r_dihedral_angle_3_deg	10.946
r_dihedral_angle_1_deg	5.958
r_angle_refined_deg	1.959
r_angle_other_deg	1.471
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.014
r_gen_planes_other	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.359
r_dihedral_angle_4_deg	22.549
r_dihedral_angle_3_deg	10.946
r_dihedral_angle_1_deg	5.958
r_angle_refined_deg	1.959
r_angle_other_deg	1.471
r_chiral_restr	0.111
r_bond_refined_d	0.017
r_gen_planes_refined	0.014
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1065
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	89

Software

Software
Software Name	Purpose
HKL-2000	data processing
SCALEPACK	data scaling
Aimless	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	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 R01GM133198.