6Z7L | pdb_00006z7l

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 with GSK789

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 MES pH 6.5, 15% v/v PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.968	α = 90
b = 48.286	β = 90
c = 61.245	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	CCD	RIGAKU SATURN A200		2017-11-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

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	1.62	37.92	91.7	0.041	17.5	2.7		15543

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.62	1.71	76.2		0.331	2.7	1.5

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	1.624	37.919	15481	750	90.872	0.185	0.1826	0.2	0.2246	0.24	18.456

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]
0.356			0.308		-0.664

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.962
r_dihedral_angle_4_deg	20.433
r_dihedral_angle_3_deg	11.461
r_dihedral_angle_1_deg	6.07
r_lrange_it	5.433
r_lrange_other	5.431
r_scangle_it	2.973
r_scangle_other	2.971
r_mcangle_it	2.439
r_mcangle_other	2.437
r_scbond_it	1.806
r_scbond_other	1.805
r_mcbond_it	1.444
r_mcbond_other	1.431
r_angle_refined_deg	1.213
r_angle_other_deg	1.212
r_nbd_refined	0.197
r_nbd_other	0.196
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.156
r_xyhbond_nbd_refined	0.14
r_symmetry_nbd_refined	0.105
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.058
r_symmetry_xyhbond_nbd_other	0.022
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1061
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	34

Software

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