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Crystal structure of human ATAD2 bromodomain in complex with 8-(((3R,4R,5S)-3-((4,4-difluorocyclohexyl)methoxy)-5-methoxypiperidin-4-yl)amino)-3-methyl-5-(5-methylpyridin-3-yl)-1,7-naphthyridin-2(1H)-one
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, 20-25% PEG3350,277K
Crystal Properties Matthews coefficient Solvent content 3.98 69.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.158 α = 90 b = 79.158 β = 90 c = 135.857 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 PILATUS3 6M 2014-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.95373 ESRF ID29
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 1.82 135.86 100 0.072 19.3 10.6 23289
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 1.82 1.92 100 0.507 5.2 11.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.82 68.55 22036 1192 99.97 0.17424 0.17378 0.1833 0.18256 0.1928 RANDOM 31.982
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] 0.02 0.01 0.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.502 r_dihedral_angle_4_deg 12.858 r_dihedral_angle_3_deg 11.017 r_long_range_B_refined 8.204 r_long_range_B_other 8.204 r_dihedral_angle_1_deg 4.183 r_scangle_other 3.402 r_mcangle_other 2.16 r_mcangle_it 2.156 r_scbond_it 1.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.502 r_dihedral_angle_4_deg 12.858 r_dihedral_angle_3_deg 11.017 r_long_range_B_refined 8.204 r_long_range_B_other 8.204 r_dihedral_angle_1_deg 4.183 r_scangle_other 3.402 r_mcangle_other 2.16 r_mcangle_it 2.156 r_scbond_it 1.991 r_scbond_other 1.986 r_mcbond_it 1.294 r_mcbond_other 1.284 r_angle_refined_deg 0.949 r_angle_other_deg 0.742 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_bond_other_d 0.003 r_gen_planes_refined 0.003 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 1084 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling