8Q34

Crystal structure of the first bromodomain of human BRD4 in complex with the ligand ZZ001229a

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	20% PEG6000 -- 10% ethylene glycol -- 0.1M HEPES pH 7.0 -- 0.2M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.239	α = 90.033
b = 44.093	β = 90
c = 78.479	γ = 90.026

Symmetry
Space Group	P 1

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 EIGER2 XE 16M		2022-11-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9763	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.48	78.479	90.9	0.994	5.7	3.4		75591

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.48	1.506	51.3		0.394

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.48	78.479	75499	3632	90.769	0.185	0.1836	0.2164	14.278

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]
1.138	-0.234	-0.503	-0.571	-0.096	-0.567

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.294
r_dihedral_angle_3_deg	14.31
r_dihedral_angle_2_deg	6.601
r_lrange_it	5.569
r_dihedral_angle_1_deg	5.469
r_lrange_other	5.319
r_scangle_it	3.533
r_scangle_other	3.533
r_angle_refined_deg	2.905
r_scbond_it	2.254
r_scbond_other	2.254
r_mcangle_it	2.185
r_mcangle_other	2.185
r_mcbond_it	1.393
r_mcbond_other	1.386
r_angle_other_deg	0.474
r_symmetry_xyhbond_nbd_refined	0.27
r_symmetry_nbd_refined	0.234
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.204
r_nbd_other	0.194
r_symmetry_nbd_other	0.192
r_nbtor_refined	0.191
r_symmetry_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.075
r_ncsr_local_group_6	0.064
r_ncsr_local_group_2	0.062
r_ncsr_local_group_5	0.058
r_ncsr_local_group_3	0.057
r_ncsr_local_group_4	0.052
r_ncsr_local_group_1	0.049
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4224
Nucleic Acid Atoms
Solvent Atoms	804
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
REFMAC	phasing