4YH3 | pdb_00004yh3

Crystal structure of human BRD4(1) in complex with 4-[(2E)-3-(4-methoxyphenyl)-2-phenylprop-2-enoyl]-3,4-dihydroquinoxalin-2(1H)-one (compound 19a)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	10% PEG3350, 0.1 M HEPES, pH 7.5, 0.2 M L-proline, soaked in 20 mM ligand for 3 hours at room temperature

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.936	α = 90
b = 44.072	β = 90
c = 78.161	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		2012-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0750	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	1.6	50	98.7	0.088	11.7	6		17723

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	1.6	1.66	100		0.664	3.5	6.1	1765

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	1.6	29.24	17608	895	97.84	0.1617	0.1597	0.17	0.1994	0.22	RANDOM	29.6066

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]
-0.04			0.05		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.146
r_dihedral_angle_4_deg	17.349
r_dihedral_angle_3_deg	13.517
r_dihedral_angle_1_deg	5.942
r_mcangle_it	3.05
r_mcbond_it	2.204
r_mcbond_other	2.155
r_angle_refined_deg	2.063
r_angle_other_deg	1.005
r_chiral_restr	0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.146
r_dihedral_angle_4_deg	17.349
r_dihedral_angle_3_deg	13.517
r_dihedral_angle_1_deg	5.942
r_mcangle_it	3.05
r_mcbond_it	2.204
r_mcbond_other	2.155
r_angle_refined_deg	2.063
r_angle_other_deg	1.005
r_chiral_restr	0.135
r_bond_refined_d	0.021
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1068
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	29

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.