9ZYT | pdb_00009zyt

Crystal Structure of BRD4 Bromodomain BD1 in Complex with Small Molecule PLX-3618

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		previously determined structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.1	293	0.2 M ammonium sulfate, 0.10 M Tris/HCl pH 8.10, 35.00% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.198	α = 90
b = 115.853	β = 90.119
c = 39.045	γ = 90

Symmetry
Space Group	P 1 21 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	Bruker PHOTON III		2021-03-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	Excillum MetalJet D2+ 70 kV	1.34138

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	1.661	23.863	98.4	0.093	0.11	0.057	0.996	8.4	3.4		31041

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	1.661	1.721	93.6		0.431	0.542	0.322	0.652	2.2	2.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.661	23.863	31040	1507	97.921	0.153	0.1501	0.1649	0.2017	0.2051	16.485

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]
-4.332		-3.598	7.668		-3.336

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.264
r_dihedral_angle_4_deg	19.445
r_dihedral_angle_3_deg	14.573
r_dihedral_angle_1_deg	7.138
r_lrange_it	4.411
r_lrange_other	4.305
r_scangle_it	2.845
r_scangle_other	2.844
r_mcangle_it	2.427
r_mcangle_other	2.426
r_angle_refined_deg	2.19
r_scbond_it	1.945
r_scbond_other	1.944
r_mcbond_it	1.713
r_mcbond_other	1.712
r_angle_other_deg	1.359
r_xyhbond_nbd_refined	0.229
r_nbd_refined	0.221
r_symmetry_xyhbond_nbd_refined	0.2
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.189
r_nbd_other	0.184
r_symmetry_nbd_refined	0.147
r_symmetry_xyhbond_nbd_other	0.135
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.017
r_gen_planes_refined	0.016
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2072
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	140

Software

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