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Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with 5-methyl uridine
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 4.09 69.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.59 α = 90 b = 79.59 β = 90 c = 138.421 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 2013-05-10 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 1.8 34.59 98.3 0.08 16.2 9.3 24186 24161 27.8
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 1.8 1.9 96.5 0.798 2.6 9.4 3381
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 1.8 30.93 2 24161 22926 1235 97.75 0.207 0.17083 0.16895 0.1782 0.20494 0.2104 RANDOM 31.416
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] -0.12 -0.12 -0.12 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.872 r_dihedral_angle_3_deg 12.903 r_dihedral_angle_4_deg 12.527 r_long_range_B_refined 9.424 r_long_range_B_other 9.422 r_dihedral_angle_1_deg 4.757 r_scangle_other 4.144 r_mcangle_other 2.727 r_mcangle_it 2.723 r_scbond_it 2.648
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.872 r_dihedral_angle_3_deg 12.903 r_dihedral_angle_4_deg 12.527 r_long_range_B_refined 9.424 r_long_range_B_other 9.422 r_dihedral_angle_1_deg 4.757 r_scangle_other 4.144 r_mcangle_other 2.727 r_mcangle_it 2.723 r_scbond_it 2.648 r_scbond_other 2.635 r_mcbond_it 1.749 r_mcbond_other 1.708 r_angle_refined_deg 1.627 r_angle_other_deg 0.942 r_chiral_restr 0.11 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 43
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling