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Crystal structure of ATAD2A bromodomain complexed with 3-(3,5-dimethyl-1,2-oxazol-4-yl)-5-[(phenylsulfonyl)amino]benzoicacid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 2.1-2.4M Ammonium Sulfate, 0.1M Bis-Tris pH 5.5, 10% Glycerol.
Crystal Properties Matthews coefficient Solvent content 4.05 69.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.288 α = 90 b = 79.288 β = 90 c = 137.945 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 193 CCD ADSC QUANTUM 315r 2014-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.73 68.665 99.9 0.1 14 16.9 27509
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.82 100 1.649 1.649 0.4 17.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DAI 1.73 61.47 27419 1379 99.7 0.185 0.184 0.197 0.2121 RANDOM 35.79
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.946 r_dihedral_angle_3_deg 12.893 r_dihedral_angle_4_deg 12.277 r_dihedral_angle_1_deg 4.369 r_mcangle_it 3.428 r_mcbond_it 2.297 r_mcbond_other 2.268 r_angle_refined_deg 1.37 r_angle_other_deg 0.814 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.946 r_dihedral_angle_3_deg 12.893 r_dihedral_angle_4_deg 12.277 r_dihedral_angle_1_deg 4.369 r_mcangle_it 3.428 r_mcbond_it 2.297 r_mcbond_other 2.268 r_angle_refined_deg 1.37 r_angle_other_deg 0.814 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_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 1084 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction