5FBX | pdb_00005fbx

Crystal structure of the first bromodomain of human BRD4 in complex with PNZ5 isoxazole inhibitor

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, SITTING DROP	7.8	277.15	20 % PEG 3350, 0.2 M zinc acetate, 0.1 M imidazole pH 7.8

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.296	α = 90
b = 44.52	β = 90
c = 79.767	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	PIXEL	DECTRIS PILATUS 6M		2015-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.85	29.71	99.6	0.095	0.046	18.9	9.6	12496	12496			15.371

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	1.85	1.89	98.1		0.998	2.3	9.7

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	1.85	29.71	11826	610	99.12	0.21516	0.21239	0.22	0.26663	0.27	RANDOM	25.265

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]
1.68			-0.23		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.651
r_dihedral_angle_4_deg	17.336
r_dihedral_angle_3_deg	14.684
r_dihedral_angle_1_deg	6.549
r_long_range_B_refined	4.359
r_long_range_B_other	4.358
r_scangle_other	2.898
r_mcangle_it	2.189
r_mcangle_other	2.187
r_angle_refined_deg	2.006
r_scbond_it	1.815
r_scbond_other	1.813
r_mcbond_it	1.403
r_mcbond_other	1.397
r_angle_other_deg	1.157
r_chiral_restr	0.382
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.002
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	1061
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	24

Software

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