5NND

Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated histone 4 peptide (H3K9ac/K14ac)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.20M Na(acetate) 0.1M BTProp pH 7.5 20.0% PEG 3350 10.0% EtGly

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.63	α = 90
b = 50.49	β = 89.99
c = 64.54	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2012-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim 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	1.61	19.82	99.2	0.081	0.081	0.041	0.041	9.9	4.9		18357

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	2.2	2.32	98.2		0.635	0.635	2.2	3	1952

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	2OSS	1.82	19.82	18357	1173	92.92	0.21015	0.20604	0.28495	RANDOM	24.332

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]
-0.78		0.08	1.03		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.748
r_dihedral_angle_3_deg	15.904
r_dihedral_angle_4_deg	15.038
r_scangle_other	9.548
r_long_range_B_other	9.072
r_long_range_B_refined	9.065
r_scbond_it	8.262
r_scbond_other	8.259
r_dihedral_angle_1_deg	6.882
r_mcangle_other	6.136
r_mcangle_it	6.131
r_mcbond_it	5.708
r_mcbond_other	5.696
r_angle_refined_deg	2.307
r_angle_other_deg	1.22
r_chiral_restr	0.15
r_bond_refined_d	0.026
r_gen_planes_refined	0.016
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2188
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	4

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building