3P5O

Crystal Structure of the First Bromodomain of Human Brd4 in complex with IBET inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OUO	PDB ENTRY 2ouo

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	0.1M NaNO3, 20% PEG 3350, 10% ethylene glycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.428	α = 90
b = 44.333	β = 90
c = 78.345	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	mirrors	2010-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.93850	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.6	78.3	95.4	0.114	10.9	6.1		17041	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.69	77.4		0.383	3.4	3.8	1956

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB ENTRY 2ouo	1.6	38.58	2	16134	861	100	0.1643	0.15699	0.15556	0.18478	RANDOM	13.314

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]
1.21			-0.31		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.949
r_dihedral_angle_3_deg	11.337
r_dihedral_angle_4_deg	5.678
r_dihedral_angle_1_deg	5
r_scangle_it	2.413
r_scbond_it	1.527
r_mcangle_it	1.379
r_angle_refined_deg	1.055
r_angle_other_deg	0.832
r_mcbond_it	0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.949
r_dihedral_angle_3_deg	11.337
r_dihedral_angle_4_deg	5.678
r_dihedral_angle_1_deg	5
r_scangle_it	2.413
r_scbond_it	1.527
r_mcangle_it	1.379
r_angle_refined_deg	1.055
r_angle_other_deg	0.832
r_mcbond_it	0.7
r_mcbond_other	0.091
r_chiral_restr	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1055
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	46

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.