4MR5

Crystal Structure of the second bromodomain of human BRD2 in complex with a quinazolinone ligand (RVX-OH)

X-RAY DIFFRACTION

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.22	α = 90
b = 72.008	β = 90
c = 32.039	γ = 90

Symmetry
Space Group	P 21 21 2

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		2013-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.52

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	1.63	19.49	99.5	0.038	0.038	21.8	4.3	15694	15616			14

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	1.63	1.72	99.5		0.17	0.17	6	3.1	2184

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.63	19.22	15687	15580	780	99.32	0.1374	0.1357	0.1698	RANDOM	15.8516

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]
0.08			-0.48		0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.242
r_dihedral_angle_4_deg	27.847
r_dihedral_angle_3_deg	11.487
r_dihedral_angle_1_deg	5.423
r_mcangle_it	2.968
r_mcbond_other	2.747
r_mcbond_it	2.745
r_angle_refined_deg	1.626
r_angle_other_deg	0.863
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.242
r_dihedral_angle_4_deg	27.847
r_dihedral_angle_3_deg	11.487
r_dihedral_angle_1_deg	5.423
r_mcangle_it	2.968
r_mcbond_other	2.747
r_mcbond_it	2.745
r_angle_refined_deg	1.626
r_angle_other_deg	0.863
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	910
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	44

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	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.