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Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with thymine
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 4.04 69.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.12 α = 90 b = 79.12 β = 90 c = 138.06 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 1.9 34.51 100 0.098 12.7 7.3 20904 20842 27.5
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 1.9 2 100 0.854 2.2 7.3 2976
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 1.9 34.33 2 20842 19771 1070 99.95 0.206 0.16897 0.1671 0.1767 0.20342 0.2082 RANDOM 31.704
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] -0.16 -0.16 -0.16 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.949 r_dihedral_angle_4_deg 20.024 r_dihedral_angle_3_deg 13.378 r_long_range_B_refined 8.951 r_long_range_B_other 8.949 r_scangle_other 4.609 r_dihedral_angle_1_deg 4.517 r_scbond_it 2.92 r_scbond_other 2.912 r_mcangle_other 2.449
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.949 r_dihedral_angle_4_deg 20.024 r_dihedral_angle_3_deg 13.378 r_long_range_B_refined 8.951 r_long_range_B_other 8.949 r_scangle_other 4.609 r_dihedral_angle_1_deg 4.517 r_scbond_it 2.92 r_scbond_other 2.912 r_mcangle_other 2.449 r_mcangle_it 2.446 r_angle_refined_deg 1.65 r_mcbond_it 1.619 r_mcbond_other 1.606 r_angle_other_deg 0.857 r_chiral_restr 0.112 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 47
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling