6S57

Crystal structure of human ATAD2 bromodomain in complex withN-(3-(azepan-1-ylsulfonyl)-4-methylphenyl)-2-(4,4-dimethyl-2,5-dioxoimidazolidin-1-yl)acetamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2780.1M trisHCl pH 7.0-8.0, 1.2-1.5M ammonium sulphate and 20-25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
4.0769.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.69α = 90
b = 79.69β = 90
c = 137.28γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2013-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97950DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8239.8598.819.79.523434
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.87

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.8239.8522226120498.330.17440.173080.19995RANDOM38.714
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]
0.280.140.28-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.201
r_dihedral_angle_4_deg12.374
r_dihedral_angle_3_deg12.289
r_long_range_B_refined8.938
r_long_range_B_other8.86
r_scangle_other5.642
r_dihedral_angle_1_deg4.481
r_scbond_it3.535
r_scbond_other3.458
r_mcangle_other3.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.201
r_dihedral_angle_4_deg12.374
r_dihedral_angle_3_deg12.289
r_long_range_B_refined8.938
r_long_range_B_other8.86
r_scangle_other5.642
r_dihedral_angle_1_deg4.481
r_scbond_it3.535
r_scbond_other3.458
r_mcangle_other3.124
r_mcangle_it3.115
r_mcbond_it2.007
r_mcbond_other1.967
r_angle_other_deg1.4
r_angle_refined_deg1.396
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1084
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling