5CPE | pdb_00005cpe

Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	277	20% PEG3350, 0.2M NaNO3, 0.1M HEPES,10% EtGhly, pH7.2

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.06	α = 90
b = 45.82	β = 96.72
c = 47.74	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	PSI PILATUS 6M		2015-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	OTHER	0.97776

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.62	47.41	98.5	0.047	0.02	0.998	31.5	6.3		16363

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.62	1.64	98		0.083	0.035	0.995	17.5	6.5	835

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		THROUGHOUT	1.62	47.41	15568	787	98.3	0.1607	0.1593	0.17	0.1868	0.19	RANDOM	15.348

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]
-0.19		-0.12	-0.03		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.314
r_dihedral_angle_4_deg	17.062
r_dihedral_angle_3_deg	12.827
r_dihedral_angle_1_deg	5.183
r_mcangle_it	1.787
r_angle_refined_deg	1.657
r_mcbond_it	1.097
r_mcbond_other	1.079
r_angle_other_deg	1.05
r_chiral_restr	0.363

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.314
r_dihedral_angle_4_deg	17.062
r_dihedral_angle_3_deg	12.827
r_dihedral_angle_1_deg	5.183
r_mcangle_it	1.787
r_angle_refined_deg	1.657
r_mcbond_it	1.097
r_mcbond_other	1.079
r_angle_other_deg	1.05
r_chiral_restr	0.363
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1082
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

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.