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ATAD2 bromodomain complexed with histone H4K5ac (res 1-10) ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TT2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 2.0 M sodium phosphate monobasic monohydrate/potassium phosphate dibasic, pH 6.6
Crystal Properties Matthews coefficient Solvent content 3.05 59.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.56 α = 90 b = 53.56 β = 90 c = 160.35 γ = 90
Symmetry Space Group P 43 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 293 CMOS RDI CMOS_8M 2020-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1 ALS 4.2.2
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 1.59 44.54 100 0.131 0.136 0.0178 1 18.87 2 32508 26.92
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 1.59 1.62 97.14 0.6612 0.935 0.6612 0.495 0.75 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4TT2 1.6 44.54 1.34 31784 1612 99.82 0.1953 0.194 0.1992 0.2187 0.2229 39.75
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 f_dihedral_angle_d 22.2272 f_angle_d 1.2503 f_chiral_restr 0.0759 f_bond_d 0.0137 f_plane_restr 0.0085
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1157 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement Coot model building XDS data reduction XDS data scaling PHASER phasing