5EGU | pdb_00005egu

FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 3-Butyl-8-(6-butyl-5,7-dimethyl-[1,2,4]triazolo[1,5-a]pyrimidin-2-ylsulfanylmethyl)-7-ethyl-3,7-dihydropurine-2,6-dione

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OSS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	Ratio 1:1 (protein:precipitant). 25 mg/mL BRD4_BD1 protein. 1.0 mM inhibitor (in DMSO) final concentration. Protein buffer: 0.01M HEPES (pH 7.5), 0.15M NaCl. Precipitant agent : 0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 25% PEG3350. Cryoprotectant : 10% ethylene glycol.

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.686	α = 90
b = 83.612	β = 90
c = 107.391	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	IMAGE PLATE	MAR scanner 345 mm plate		2006-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.541790

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	2.2	50	97.8	0.104	13.15	4.63		59187

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	2.21	2.35	95.2		0.48	3.44	4.52

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	2OSS	2.21	45.18	29752	1566	97.87	0.18724	0.18474	0.19	0.2353	0.24	RANDOM	25.187

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]
0.39			0.67		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.462
r_dihedral_angle_4_deg	14.513
r_dihedral_angle_3_deg	14.214
r_dihedral_angle_1_deg	6.442
r_long_range_B_refined	5.644
r_long_range_B_other	5.644
r_scangle_other	4.27
r_mcangle_it	3.246
r_mcangle_other	3.246
r_scbond_it	2.7
r_scbond_other	2.699
r_mcbond_it	2.154
r_mcbond_other	2.151
r_angle_refined_deg	1.832
r_angle_other_deg	1.289
r_chiral_restr	0.099
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3934
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	140

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
REFMAC	refinement