8PXN | pdb_00008pxn

N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH (1R,1'R)-7,7'-(ethane-1,2-diylbis(oxy))bis(1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in house structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.1M Tris pH8.5, 12% w/v 4K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.265	α = 89.973
b = 41.879	β = 89.948
c = 105.383	γ = 89.882

Symmetry
Space Group	P 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	CCD	RIGAKU SATURN A200		2016-09-16	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)	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	1.95	52.69	92.8	0.043	0.975	18.3	2.1		35040

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	1.95	2.18	90.6		0.128	0.878	6.7	2.1

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	1.952	35.128	34031	1609	90.388	0.196	0.192	0.24	0.2701	0.34	16.077

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]
0.145	-2.068	8.773	4.455	-3.615	-4.601

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.625
r_dihedral_angle_6_deg	15.435
r_dihedral_angle_1_deg	7.087
r_dihedral_angle_2_deg	6.068
r_angle_refined_deg	1.403
r_angle_other_deg	0.454
r_xyhbond_nbd_refined	0.259
r_symmetry_xyhbond_nbd_refined	0.249
r_nbd_refined	0.241
r_symmetry_nbd_other	0.199
r_nbd_other	0.19
r_nbtor_refined	0.189
r_symmetry_nbd_refined	0.173
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.076
r_chiral_restr	0.063
r_xyhbond_nbd_other	0.047
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4226
Nucleic Acid Atoms
Solvent Atoms	770
Heterogen Atoms	72

Software

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