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Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) with bound DMSO
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 4.05 69.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.248 α = 90 b = 79.248 β = 90 c = 138.189 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 2011-12-06 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 19.91 98.5 0.119 9.4 5.6 24099 24039 20.7
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 1.8 1.9 98.1 0.842 2 5.6 3405
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 19.12 2 24039 22813 1226 98.26 0.186 0.15974 0.15791 0.165 0.19366 0.2015 RANDOM 26.864
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] -0.04 -0.02 -0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.994 r_dihedral_angle_4_deg 18.203 r_dihedral_angle_3_deg 12.304 r_dihedral_angle_1_deg 4.813 r_angle_refined_deg 1.606 r_angle_other_deg 0.98 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.994 r_dihedral_angle_4_deg 18.203 r_dihedral_angle_3_deg 12.304 r_dihedral_angle_1_deg 4.813 r_angle_refined_deg 1.606 r_angle_other_deg 0.98 r_chiral_restr 0.109 r_bond_refined_d 0.016 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 218 Heterogen Atoms 61
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling