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Crystal structure of human ATAD2 bromodomain in complex with 4-((3R, 4R)-4-3-methyl-5-(5-methylpyridin-3-yl)-2-oxo-1,2-dihydroquinolin-8- yl-aminopiperidin-3-yloxymethyl)-1-thiane-1,1-dione
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 277 0.05M TRIS PH 7.5, 20-25% PEG3350. 1.5M AMSO4 4C
Crystal Properties Matthews coefficient Solvent content 4.03 69.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.172 α = 90 b = 79.172 β = 90 c = 137.617 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 2013-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
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 2.09 137.62 100 0.1 24.3 11 15746 2
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 2.09 2.21 100 0.54 5.3 10.9
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT NONE 2.09 137.62 14894 783 99.81 0.17237 0.17041 0.21064 0.1961 RANDOM 37.717
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] -0.11 -0.06 -0.11 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.107 r_dihedral_angle_3_deg 12.235 r_dihedral_angle_4_deg 9.947 r_dihedral_angle_1_deg 4.307 r_angle_refined_deg 0.915 r_angle_other_deg 0.851 r_chiral_restr 0.05 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.107 r_dihedral_angle_3_deg 12.235 r_dihedral_angle_4_deg 9.947 r_dihedral_angle_1_deg 4.307 r_angle_refined_deg 0.915 r_angle_other_deg 0.851 r_chiral_restr 0.05 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1081 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling