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Crystal structure of ATAD2A bromodomain complexed with methyl 3-amino-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzoate
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 pH5.5, 10% Glycerol
Crystal Properties Matthews coefficient Solvent content 4.04 69.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.31 α = 90 b = 79.31 β = 90 c = 137.381 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 2013-06-20 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 Merge I (Observed) Rpim I (All) CC (Half) 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 48.57 100 0.083 0.018 0.999 25 21.2 24459
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 100 0.98 0.28 0.804 2.5 13 1411
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DAI 1.8 68.68 24396 1244 99.96 0.184 0.1833 0.1931 0.197 0.2036 RANDOM 30.077
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.521 r_dihedral_angle_4_deg 14.334 r_dihedral_angle_3_deg 13.296 r_dihedral_angle_1_deg 4.329 r_mcangle_it 2.975 r_mcbond_it 1.954 r_mcbond_other 1.946 r_angle_refined_deg 1.482 r_angle_other_deg 0.844 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.521 r_dihedral_angle_4_deg 14.334 r_dihedral_angle_3_deg 13.296 r_dihedral_angle_1_deg 4.329 r_mcangle_it 2.975 r_mcbond_it 1.954 r_mcbond_other 1.946 r_angle_refined_deg 1.482 r_angle_other_deg 0.844 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 253 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction