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Crystal structure of human ATAD2 bromodomain in complex with 8-(((1R,2R,3R,5S)-2-(2-(1,1-dioxidotetrahydro-2H-thiopyran-4-yl)ethyl)-8-azabicyclo[3.2.1]octan-3-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)quinolin-2(1H)-one
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 0.1M trisHCl pH 7.0-8.0, 1.2-1.5M ammonium sulphate and 20-25% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.96 68.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.254 α = 90 b = 79.254 β = 90 c = 135.033 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 CCD RIGAKU SATURN A200 2013-10-22 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) 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 2.61 135.03 99.6 20.8 10.3 8153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.61 2.75 100 10.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 2.61 37.64 7735 374 99.82 0.18646 0.18427 0.1906 0.23194 0.2306 RANDOM 48.947
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] 0.28 0.14 0.28 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.451 r_dihedral_angle_4_deg 21.687 r_dihedral_angle_3_deg 16.005 r_long_range_B_refined 12.261 r_long_range_B_other 12.102 r_scangle_other 11.181 r_mcangle_it 8.049 r_mcangle_other 8.043 r_scbond_it 7.831 r_scbond_other 7.741
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.451 r_dihedral_angle_4_deg 21.687 r_dihedral_angle_3_deg 16.005 r_long_range_B_refined 12.261 r_long_range_B_other 12.102 r_scangle_other 11.181 r_mcangle_it 8.049 r_mcangle_other 8.043 r_scbond_it 7.831 r_scbond_other 7.741 r_mcbond_it 5.908 r_mcbond_other 5.725 r_dihedral_angle_1_deg 5.7 r_angle_refined_deg 1.48 r_angle_other_deg 0.956 r_chiral_restr 0.077 r_gen_planes_refined 0.05 r_bond_refined_d 0.015 r_bond_other_d 0.007 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1077 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling