3UVW | pdb_00003uvw

Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H4K5acK8ac)

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 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	278	0.1M Tris, 20% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 278K, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.5	α = 90
b = 47.28	β = 90
c = 59.53	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		2010-10-17	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	1.37	37.01	99.6	0.1	0.1	10	5.5	25922	25818			11.7

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	1.37	1.44	97.2		0.52	0.52	1.5	3.1	3617

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 PDB Entries 2OSS, 2OUO, 2GRC, 2OO1, 3DAI, 3D7C	1.37	37.01	25894	25770	1312	99.52	0.1269	0.1269	0.1246	0.13	0.1711	0.17	RANDOM	14.0345

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]
0.02			0.27		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.121
r_dihedral_angle_4_deg	14.141
r_sphericity_free	13.067
r_dihedral_angle_3_deg	12.196
r_scangle_it	8.004
r_scbond_it	5.897
r_dihedral_angle_1_deg	5.85
r_sphericity_bonded	5.188
r_mcangle_it	4.5
r_mcbond_it	3.489
r_rigid_bond_restr	2.815
r_mcbond_other	2.067
r_angle_other_deg	1.645
r_angle_refined_deg	1.637
r_chiral_restr	0.111
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1137
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	4

Software

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