6YB4 | pdb_00006yb4

Crystal structure of human ATAD2 bromodomain in complex with N-(4-bromo-3-(3-methylpyrrolidin-1-yl)sulfonyl)phenyl)-2-(-4-cyclopropyl-4-methyl-2,5-dioxoimidazolidin-1-yl)acetamide

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1M trisHCl pH 7.0-8.0, 1.2-1.5M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
4.06	69.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.407	α = 90
b = 79.407	β = 90
c = 137.969	γ = 120

Symmetry
Space Group	P 65 2 2

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 PILATUS 6M-F		2017-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

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	1.85	68.77	99.2	0.062	1	20.7	18.9		22564

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	1.85	1.95			0.508	0.961	6.1

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	FOURIER SYNTHESIS	FREE R-VALUE	1.85	68.768	22534	1120	99.194	0.191	0.1902	0.2	0.2152	0.22	30.81

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]
0.141	0.07		0.141		-0.457

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.184
r_dihedral_angle_3_deg	13.759
r_dihedral_angle_4_deg	9.97
r_lrange_it	8.614
r_lrange_other	8.611
r_scangle_it	5.868
r_scangle_other	5.865
r_dihedral_angle_1_deg	4.427
r_scbond_it	3.68
r_scbond_other	3.324
r_mcangle_other	3.07
r_mcangle_it	3.064
r_mcbond_it	2.082
r_mcbond_other	2.068
r_angle_other_deg	1.228
r_angle_refined_deg	1.178
r_xyhbond_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.2
r_nbd_refined	0.188
r_nbd_other	0.181
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.157
r_symmetry_nbd_refined	0.118
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.059
r_bond_refined_d	0.004
r_gen_planes_refined	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	1084
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	53

Software

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