6FO5 | pdb_00006fo5

FIRST DOMAIN OF HUMAN BROMODOMAIN BRD4 IN COMPLEX WITH INHIBITOR #17

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	EVAPORATION	8.5	292	2.5mM of #17 inhibitor (in DMSO) final concentration. Ratio 1:1 (protein:precipitant. 12mg/mL of BRD4(BD1) protein. Precipitant agent: 0.3M NaNO3; 0.1M NaCl; 22% (w/v) PEG3350; 10% (w/v) ethylene glycol. Cryoprotectant: 10 % (w/v) glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.284	α = 90
b = 47.498	β = 90
c = 58.468	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		2016-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	0.95	36.87	99.61	0.04761	0.05153	0.01942	0.999	16.41	6.8		78067			9.83

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.95	0.98	96.26		1.617	1.819	0.8059	0.434	0.78	4.7

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	0.95	36.87	74651	3929	99.28	0.13641	0.1355	0.14	0.15362	0.16	RANDOM	15.31

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]
0.24			-1.34		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.261
r_sphericity_free	26.476
r_dihedral_angle_4_deg	24.807
r_sphericity_bonded	15.939
r_dihedral_angle_3_deg	12.601
r_mcbond_other	10.281
r_mcbond_it	10.274
r_mcangle_it	8.821
r_mcangle_other	8.815
r_rigid_bond_restr	8.803
r_long_range_B_refined	7.169
r_long_range_B_other	7.167
r_scangle_other	6.845
r_dihedral_angle_1_deg	5.513
r_scbond_it	4.9
r_scbond_other	4.898
r_angle_refined_deg	2.363
r_angle_other_deg	1.697
r_chiral_restr	0.18
r_bond_refined_d	0.03
r_gen_planes_refined	0.014
r_bond_other_d	0.006
r_gen_planes_other	0.006
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	173
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
Coot	model building
PHASER	phasing