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ATAD2 in complex with PepLite-Ile
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 6.5 293 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.539 α = 90 b = 79.539 β = 90 c = 138.471 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 PIXEL DECTRIS PILATUS 6M 2019-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.976 Diamond I04-1
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 1.53 61.67 100 0.145 0.152 0.044 0.998 11.6 21.6 39838
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 1.53 1.56 9.936 10.474 3.3 0.33 19.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DAI 1.53 61.67 39764 1952 99.96 0.192 0.1907 0.1911 0.2156 0.2149 35.161
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] 0.646 0.323 0.646 -2.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.093 r_dihedral_angle_4_deg 16.171 r_dihedral_angle_3_deg 15.993 r_lrange_other 11.63 r_lrange_it 11.607 r_scangle_it 8.516 r_scangle_other 8.512 r_scbond_it 5.79 r_scbond_other 5.264 r_dihedral_angle_1_deg 4.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.093 r_dihedral_angle_4_deg 16.171 r_dihedral_angle_3_deg 15.993 r_lrange_other 11.63 r_lrange_it 11.607 r_scangle_it 8.516 r_scangle_other 8.512 r_scbond_it 5.79 r_scbond_other 5.264 r_dihedral_angle_1_deg 4.987 r_mcangle_it 4.125 r_mcangle_other 4.124 r_mcbond_other 2.905 r_mcbond_it 2.901 r_angle_refined_deg 1.836 r_angle_other_deg 1.489 r_symmetry_nbd_refined 0.282 r_symmetry_xyhbond_nbd_refined 0.253 r_xyhbond_nbd_refined 0.239 r_nbd_other 0.236 r_nbd_refined 0.223 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_other 0.099 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.08 r_xyhbond_nbd_other 0.015 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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 206 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing