3S91 | pdb_00003s91

Crystal Structure of the first bromodomain of human BRD3 in complex with the inhibitor JQ1

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	14% isopropanol, 0.14M CaCl2, 30% glycerol, 0.7M acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.56	α = 90
b = 86.56	β = 90
c = 76.891	γ = 120

Symmetry
Space Group	P 65 2 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		2010-04-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5

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	2.06	28.743	99.9	0.097	0.097	13.2	5.6	11022	11011			32

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	2.06	2.17	99.9		0.809	0.809	1	5.2	1552

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	PDB entry 2NXB	2.06	28.74	10990	10985	526	99.95	0.1968	0.1968	0.195	0.2	0.2325	0.23	RANDOM	37.3817

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]
1.69	0.84		1.69		-2.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.788
r_dihedral_angle_3_deg	14.088
r_dihedral_angle_4_deg	9.667
r_dihedral_angle_1_deg	4.427
r_angle_refined_deg	1.626
r_angle_other_deg	0.969
r_chiral_restr	0.083
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.788
r_dihedral_angle_3_deg	14.088
r_dihedral_angle_4_deg	9.667
r_dihedral_angle_1_deg	4.427
r_angle_refined_deg	1.626
r_angle_other_deg	0.969
r_chiral_restr	0.083
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	879
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	35

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.