8C11 | pdb_00008c11

BRD4 in complex with 2-(2-(4-(3,5-dimethylisoxazol-4-yl)-1H-pyrazol-1-yl)acetamido)-N-ethylpropanamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	5LRQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.144	α = 90
b = 43.237	β = 90
c = 79.276	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	Bruker PHOTON III		2022-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.8	18.023	99.8	0.076	0.992	8.3	6.3		12689

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	99.5		0.856	0.54	1.4	3.5

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5LRQ	1.8	18.023	12646	645	99.677	0.197	0.1948	0.2	0.2341	0.24	13.388

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]
0.31			-0.655		0.345

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.4
r_dihedral_angle_3_deg	15.151
r_dihedral_angle_2_deg	12.096
r_dihedral_angle_1_deg	6.212
r_lrange_it	5.572
r_lrange_other	5.556
r_scangle_it	2.818
r_scangle_other	2.817
r_scbond_it	1.902
r_scbond_other	1.901
r_mcangle_other	1.727
r_mcangle_it	1.722
r_angle_refined_deg	1.55
r_mcbond_it	1.08
r_mcbond_other	1.079
r_angle_other_deg	0.772
r_symmetry_nbd_refined	0.296
r_nbd_other	0.288
r_nbd_refined	0.247
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.189
r_xyhbond_nbd_refined	0.157
r_symmetry_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.074
r_gen_planes_other	0.012
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1081
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
PROTEUM PLUS	data reduction
Aimless	data scaling
PHASER	phasing