5DLZ | pdb_00005dlz

FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR 4-[(1-methyl-2-oxo-1,2-dihydroquinolin-4-yl)oxy]-N-({1-[(3-methylphe methyl]piperidin-4-yl}methyl)butanamide

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	7.5	292	Ratio 1:1 (protein:precipitant) 12 mg/mL Brd4_BD1 protein. Protein buffer 10 mM HEPES (pH 7.5) 150 mM NaCl.Precipitant agent 22 % (w/v) PEG 3350, 10% (w/v) ethylene glycol 30 % (w/v), 0.3 M NaNO3. 5.0 mM inhibitor (in DMSO) final concentration. Cryoprotection with 10% (w/v) glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.263	α = 90
b = 44.236	β = 90
c = 78.436	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 2M		2006-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	50	96.3	0.149	7.54	4.47		14342

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.8	95.2		0.421	4.15	4.38

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	1.7	39.22	13624	718	96.29	0.25529	0.25122	0.26	0.3339	0.33	RANDOM	12.795

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]
2.46			-1.01		-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.371
r_dihedral_angle_4_deg	24.098
r_sphericity_free	19.76
r_dihedral_angle_3_deg	14.115
r_sphericity_bonded	8.873
r_dihedral_angle_1_deg	7.868
r_long_range_B_refined	3.128
r_long_range_B_other	3.096
r_scangle_other	3.087
r_scbond_it	2.576
r_scbond_other	2.574
r_rigid_bond_restr	2.423
r_angle_refined_deg	2.329
r_mcangle_it	2.251
r_mcangle_other	2.251
r_mcbond_it	1.957
r_mcbond_other	1.949
r_angle_other_deg	1.473
r_chiral_restr	0.135
r_bond_refined_d	0.028
r_gen_planes_refined	0.012
r_bond_other_d	0.007
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1062
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	34

Software

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