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Crystal structure of the bromodomain of ATAD2 with triazolopyridazine (cpd 22)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.25 293 ATAD2 (981-1108) at 12 mg/ml in 25 mM Tris pH 9.7, 300 mM NaCl, 0.5 mM TCEP crystallised from 20% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.25. Ligands were introduced by soaking, cryo-protection with 20 % glycerol.
Crystal Properties Matthews coefficient Solvent content 4.05 69.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.291 α = 90 b = 79.291 β = 90 c = 138.014 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 CCD RIGAKU SATURN 944+ 2015-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.96 48.68 92.4 0.053 0.06 0.026 0.999 22.3 4.8 17803 27.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.06 95.4 0.405 0.507 0.299 0.751 2.5
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 internal model 1.96 48.68 17671 897 92.43 0.1914 0.1904 0.1893 0.2103 0.214 RANDOM 32.66
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] 1.2148 1.2148 -2.4296
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.78 t_omega_torsion 2.69 t_angle_deg 0.89 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.78 t_omega_torsion 2.69 t_angle_deg 0.89 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 49
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction AMoRE phasing