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Crystal structure of human ATAD2 bromodomain in complex with 4-(3R,4R) -4-(3-methyl-2-oxo-1,2-dihydro-1,7-naphthyridin-8-yl)aminopiperidin-3- yloxymethyl)-1-thiane-1,1-dione
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M TRISHCL PH 7.0-8.0, 1.2-1.5M AMMONIUM SULPHATE AND 20-25% PEG3350
Crystal Properties Matthews coefficient Solvent content 4.01 69.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.17 α = 90 b = 79.17 β = 90 c = 137.13 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 2013-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.86 68.56 94.9 0.09 14.2 11 20685 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 1.86 1.91 96.7 0.72 2.9 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 MOLECULAR REPLACEMENT THROUGHOUT 1.86 61.33 19586 1058 93.59 0.18243 0.18115 0.1875 0.20769 0.2143 RANDOM 31.89
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] -0.13 -0.06 -0.13 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.694 r_dihedral_angle_4_deg 13.651 r_dihedral_angle_3_deg 12.449 r_dihedral_angle_1_deg 4.049 r_angle_refined_deg 0.878 r_angle_other_deg 0.779 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.694 r_dihedral_angle_4_deg 13.651 r_dihedral_angle_3_deg 12.449 r_dihedral_angle_1_deg 4.049 r_angle_refined_deg 0.878 r_angle_other_deg 0.779 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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 197 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling