5D0C | pdb_00005d0c

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MXF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly,pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.03	α = 90
b = 46.27	β = 96.74
c = 47.44	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	CCD	ADSC QUANTUM 315		2014-09-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97915	SSRF	BL17U

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	1.49	47.11	90.8	0.06	0.026	0.996	23.9	7		19102

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	1.49	1.52	96.5		0.1	0.041	0.993	15.2	6.9	986

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3MXF	1.49	47.11	18213	874	90.69	0.1654	0.1645	0.17	0.1833	0.19	RANDOM	15.264

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]
-0.32		-0.26	0.47		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.395
r_dihedral_angle_3_deg	12.899
r_dihedral_angle_4_deg	9.624
r_dihedral_angle_1_deg	5.043
r_mcangle_it	1.683
r_angle_refined_deg	1.583
r_angle_other_deg	1.054
r_mcbond_it	1.029
r_mcbond_other	1.028
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.395
r_dihedral_angle_3_deg	12.899
r_dihedral_angle_4_deg	9.624
r_dihedral_angle_1_deg	5.043
r_mcangle_it	1.683
r_angle_refined_deg	1.583
r_angle_other_deg	1.054
r_mcbond_it	1.029
r_mcbond_other	1.028
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1072
Nucleic Acid Atoms
Solvent Atoms	115
Heterogen Atoms	55

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
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.