4YH4 | pdb_00004yh4

Crystal structure of human BRD4(1) in complex with 4-[(5-phenylpyridin-3-yl)carbonyl]-3,4-dihydroquinoxalin-2(1H)-one (compound 19d)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	0.2 M potassium thiocyanate, 20% w/v PEG3350, 0.6 mM ligand

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.799	α = 90
b = 44.436	β = 90
c = 77.353	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		2012-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9300	NSLS	X29A

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	1.33	50	99.9	0.067	17.8	13.8		30557

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	1.33	1.38	100		0.308	11.3	14	2983

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	1.33	33.96	30417	1538	99.58	0.1093	0.1073	0.11	0.1466	0.15	RANDOM	17.0817

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]
0.1			0.04		-0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.889
r_sphericity_free	33.12
r_dihedral_angle_3_deg	12.79
r_sphericity_bonded	12.053
r_dihedral_angle_4_deg	11.144
r_dihedral_angle_1_deg	6.234
r_rigid_bond_restr	5.953
r_angle_refined_deg	2.316
r_mcangle_it	2.156
r_mcbond_it	1.772

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.889
r_sphericity_free	33.12
r_dihedral_angle_3_deg	12.79
r_sphericity_bonded	12.053
r_dihedral_angle_4_deg	11.144
r_dihedral_angle_1_deg	6.234
r_rigid_bond_restr	5.953
r_angle_refined_deg	2.316
r_mcangle_it	2.156
r_mcbond_it	1.772
r_mcbond_other	1.59
r_angle_other_deg	1.371
r_chiral_restr	0.129
r_bond_refined_d	0.024
r_gen_planes_refined	0.014
r_gen_planes_other	0.007
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1061
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	32

Software

Software
Software Name	Purpose
HKL-2000	data reduction
PDB_EXTRACT	data extraction
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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.