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Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) complexed with Histone H4-K(ac)12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAI pdb id: 3DAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277.15 apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 3.86 68.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.98 α = 90 b = 78.98 β = 90 c = 139.02 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 IMAGE PLATE RIGAKU RAXIS IV 2012-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 1.7 34.34 98.2 0.07 15.8 6.7 28321 28319 23.7
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 1.7 1.79 94.9 0.665 2.4 5.9 3895
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb id: 3DAI 1.7 34.34 2 28319 26877 1441 97.82 0.189 0.16319 0.16231 0.1719 0.17952 0.1889 RANDOM 25.379
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] 0.03 0.03 0.03 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.31 r_dihedral_angle_4_deg 17.258 r_dihedral_angle_3_deg 13.608 r_long_range_B_refined 9.986 r_long_range_B_other 9.984 r_dihedral_angle_1_deg 4.843 r_scangle_other 3.156 r_scbond_it 2.107 r_scbond_other 2.107 r_mcangle_other 1.815
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.31 r_dihedral_angle_4_deg 17.258 r_dihedral_angle_3_deg 13.608 r_long_range_B_refined 9.986 r_long_range_B_other 9.984 r_dihedral_angle_1_deg 4.843 r_scangle_other 3.156 r_scbond_it 2.107 r_scbond_other 2.107 r_mcangle_other 1.815 r_mcangle_it 1.794 r_angle_refined_deg 1.548 r_mcbond_it 1.173 r_mcbond_other 1.081 r_angle_other_deg 0.849 r_chiral_restr 0.105 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1116 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 49
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling