3UW9

Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K8acK12ac)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OSS	Ensemble of PDB entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C
experimental model	PDB	2OUO	Ensemble of PDB entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C
experimental model	PDB	2GRC	Ensemble of PDB entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C
experimental model	PDB	2OO1	Ensemble of PDB entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C
experimental model	PDB	3DAI	Ensemble of PDB entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C
experimental model	PDB	3D7C	Ensemble of PDB entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	0.1M Tris, 0.3M LiCl 15% PEG6000, 10% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.6	α = 90
b = 99.6	β = 90
c = 136.7	γ = 90

Symmetry
Space Group	P 41 21 2

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	ADSC QUANTUM 315r		2010-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9763	Diamond	I04

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	2.3	42.33	100	0.146	0.146	9.3	9	31295	31295			48.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	100		0.98	0.98	0.8	8.8	4501

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Ensemble of PDB entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C	2.3	42.33	31256	31231	1575	99.92	0.2026	0.2026	0.1998	0.257	RANDOM	53.129

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]
0.16			0.16		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.372
r_dihedral_angle_3_deg	16.701
r_dihedral_angle_4_deg	13.154
r_dihedral_angle_1_deg	5.605
r_angle_other_deg	1.688
r_angle_refined_deg	1.682
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.372
r_dihedral_angle_3_deg	16.701
r_dihedral_angle_4_deg	13.154
r_dihedral_angle_1_deg	5.605
r_angle_other_deg	1.688
r_angle_refined_deg	1.682
r_chiral_restr	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3792
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection
MOSFLM	data reduction

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.