4XYA | pdb_00004xya

Crystal Structure of the first bromodomain of human BRD4 in complex with a 2-amine-9H-purine ligand

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 8.5, 0.2M sodium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.242	α = 90
b = 44.373	β = 90
c = 79.015	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	APEX II CCD		2014-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	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	2.05	44.37	99.9	0.08	0.08	12.37	4.73		8708

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	2.05	2.09	99.7		0.235		3.05

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	2.05	39.51	8237	433	99.93	0.1496	0.1466	0.16	0.2068	0.22	RANDOM	14.528

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]
0.48			-0.39		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.111
r_dihedral_angle_3_deg	12.633
r_dihedral_angle_4_deg	12.214
r_sphericity_bonded	11.348
r_dihedral_angle_1_deg	5.779
r_mcangle_it	2.701
r_mcbond_it	1.808
r_mcbond_other	1.807
r_angle_refined_deg	1.652
r_angle_other_deg	0.915

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.111
r_dihedral_angle_3_deg	12.633
r_dihedral_angle_4_deg	12.214
r_sphericity_bonded	11.348
r_dihedral_angle_1_deg	5.779
r_mcangle_it	2.701
r_mcbond_it	1.808
r_mcbond_other	1.807
r_angle_refined_deg	1.652
r_angle_other_deg	0.915
r_chiral_restr	0.109
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1056
Nucleic Acid Atoms
Solvent Atoms	148
Heterogen Atoms	24

Software

Software
Software Name	Purpose
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.