6Z7M

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 (3R,4R)-N-cyclohexyl-4-((3-methyl-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl)amino)piperidine-3-carboxamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG6K

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.43	α = 90
b = 48.98	β = 90
c = 61.24	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	DECTRIS PILATUS3 6M		2013-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9200	Diamond	I04-1

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	1.26	16.66	99.1	0.043	0.999	27.4	6.2		35636

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	1.26	1.29	95.5		0.551	0.818	2.5

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	in house structure	1.26	16.657	35566	1782	98.858	0.197	0.1957	0.2	0.2138	0.22	19.953

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]
0.482			0.325		-0.807

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.481
r_dihedral_angle_3_deg	11.934
r_dihedral_angle_4_deg	9.661
r_lrange_it	5.513
r_dihedral_angle_1_deg	4.919
r_lrange_other	4.886
r_scangle_it	2.353
r_scangle_other	2.351
r_mcangle_it	1.923
r_mcangle_other	1.921
r_scbond_other	1.395
r_scbond_it	1.394
r_angle_other_deg	1.176
r_angle_refined_deg	1.159
r_mcbond_it	1.132
r_mcbond_other	1.132
r_nbd_refined	0.185
r_symmetry_nbd_refined	0.182
r_nbtor_refined	0.169
r_nbd_other	0.168
r_symmetry_nbd_other	0.162
r_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_refined	0.064
r_chiral_restr	0.055
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1046
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms	28

Software

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