5KU3 | pdb_00005ku3

BRD4 bromodomain in complex with Cpd59 ((S)-1-(3-((2-fluoro-4-(1-methyl-1H-pyrazol-4-yl)phenyl)amino)-1-(tetrahydrofuran-3-yl)-6,7-dihydro-1H-pyrazolo[4,3-c]pyridin-5(4H)-yl)ethanone)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	287	0.1 M Bis-Tris pH 6.8, 18% PEG 3350, 20% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.037	α = 90
b = 53.115	β = 90
c = 106.745	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	CCD	ADSC QUANTUM 4		2016-01-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	1.0	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.14	50	97.6	0.116	6.2	3.9		47352

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	1.14	1.18	97.9		0.633	0.744		3.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.14	50	44593	2383	97.68	0.1645	0.1635	0.17	0.1824	0.19	RANDOM	19.09

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]
-0.55			0.63		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.761
r_sphericity_free	20.511
r_dihedral_angle_4_deg	16.137
r_dihedral_angle_3_deg	11.778
r_rigid_bond_restr	8.015
r_sphericity_bonded	7.227
r_dihedral_angle_1_deg	5.227
r_angle_other_deg	3.325
r_mcangle_it	1.808
r_mcbond_it	1.703

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.761
r_sphericity_free	20.511
r_dihedral_angle_4_deg	16.137
r_dihedral_angle_3_deg	11.778
r_rigid_bond_restr	8.015
r_sphericity_bonded	7.227
r_dihedral_angle_1_deg	5.227
r_angle_other_deg	3.325
r_mcangle_it	1.808
r_mcbond_it	1.703
r_mcbond_other	1.69
r_angle_refined_deg	1.507
r_chiral_restr	0.109
r_bond_refined_d	0.009
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1048
Nucleic Acid Atoms
Solvent Atoms	202
Heterogen Atoms	76

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.