3UVY | pdb_00003uvy

Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K16acK20ac)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	278	0.2M NaI, 0.1M BTProp, 20% PEG 3350, 10% EtGly, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
1.71	28.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.225	α = 90
b = 50.478	β = 90
c = 51.969	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	ADSC QUANTUM 315r		2011-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9793	Diamond	I03

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	2.02	43.225	99.7	0.135	0.135	8.6	4.2	7890	7866			22.9

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	2.02	2.13	100		0.831	0.831	0.9	4.4	1118

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Ensemble of 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C	2.02	43.22	7857	7828	459	99.63	0.1856	0.1856	0.1811	0.19	0.2582	0.26	RANDOM	28.0894

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]
2.16			-1.92		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.371
r_dihedral_angle_3_deg	14.719
r_scangle_it	11.273
r_scbond_it	9.15
r_dihedral_angle_4_deg	6.687
r_mcangle_it	5.857
r_dihedral_angle_1_deg	5.585
r_mcbond_it	4.034
r_angle_refined_deg	1.525
r_mcbond_other	1.264
r_angle_other_deg	1.009
r_chiral_restr	0.081
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1001
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms

Software

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