8WY7

Crystal Structure of the first bromodomain of human BRD4 in complex with the inhibitor 22

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	2.0 M Sodium formate, 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
3.78	67.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.15	α = 90
b = 140.15	β = 90
c = 134.299	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 6M		2023-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL10U2	0.97918	SSRF	BL10U2

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	2.83	134.3	94.7	0.208	0.214	0.052	0.998	20	17.5		18153

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	2.83	2.98		100	0.949	0.971	0.204	0.803		20.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.83	121.37	17230	884	94.72	0.20842	0.20494	0.28074	RANDOM	88.464

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]
-0.64	-0.32		-0.64		2.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.899
r_dihedral_angle_3_deg	16.944
r_dihedral_angle_4_deg	16.392
r_long_range_B_refined	12.66
r_long_range_B_other	12.659
r_scangle_other	10.361
r_mcangle_it	9.597
r_mcangle_other	9.595
r_scbond_it	7.149
r_scbond_other	7.146
r_mcbond_it	6.915
r_mcbond_other	6.912
r_dihedral_angle_1_deg	6.456
r_angle_refined_deg	1.87
r_angle_other_deg	1.124
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.004
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	2731
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	120

Software

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