4HBW

Crystal Structure of the first bromodomain of human BRD4 in complex with a quinazoline ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OSS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.20M K3(cit), 0.1M BTProp pH 8.5, 20.0% PEG 3350, 10.0% EtGly, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.65	α = 90
b = 46.02	β = 90
c = 77.31	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	IMAGE PLATE	RIGAKU RAXIS IV		2010-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.685	29.6	100	0.097	0.097	9.1	4.5	15402	15402			22.2

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	1.68	1.78	100		0.592	0.592	1.3	4.3	2189

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	2OSS	1.69	29.6	15359	15356	767	99.98	0.1769	0.1769	0.1744	0.2283	RANDOM	20.7642

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]
1.61			-0.71		-0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.999
r_dihedral_angle_4_deg	29.497
r_dihedral_angle_3_deg	13.805
r_scangle_it	7.243
r_scbond_it	6.206
r_dihedral_angle_1_deg	5.168
r_mcangle_it	3.919
r_mcbond_it	2.572
r_angle_refined_deg	1.575
r_angle_other_deg	0.947

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.999
r_dihedral_angle_4_deg	29.497
r_dihedral_angle_3_deg	13.805
r_scangle_it	7.243
r_scbond_it	6.206
r_dihedral_angle_1_deg	5.168
r_mcangle_it	3.919
r_mcbond_it	2.572
r_angle_refined_deg	1.575
r_angle_other_deg	0.947
r_mcbond_other	0.909
r_chiral_restr	0.333
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1047
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	23

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	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.