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ATAD2 in complex with PepLite-Ala
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 = 79.435 α = 90 b = 79.435 β = 90 c = 137.648 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 0.9762 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 1.5 61.54 99.5 0.113 0.118 0.035 0.998 11.9 20.9 41568
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 1.5 1.53 2.977 3.163 1.048 0.405 16.8
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 1.5 48.702 41518 2026 99.337 0.191 0.1896 0.1897 0.2193 0.2194 34.712
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] -0.044 -0.022 -0.044 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.301 r_dihedral_angle_4_deg 15.911 r_dihedral_angle_3_deg 15.556 r_lrange_other 11.14 r_lrange_it 11.11 r_scangle_it 8.704 r_scangle_other 8.699 r_scbond_it 6.074 r_scbond_other 5.26 r_dihedral_angle_1_deg 5.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.301 r_dihedral_angle_4_deg 15.911 r_dihedral_angle_3_deg 15.556 r_lrange_other 11.14 r_lrange_it 11.11 r_scangle_it 8.704 r_scangle_other 8.699 r_scbond_it 6.074 r_scbond_other 5.26 r_dihedral_angle_1_deg 5.011 r_mcangle_other 4.088 r_mcangle_it 4.084 r_mcbond_it 2.872 r_mcbond_other 2.868 r_angle_refined_deg 1.923 r_angle_other_deg 1.544 r_symmetry_xyhbond_nbd_refined 0.305 r_nbd_other 0.249 r_xyhbond_nbd_refined 0.24 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.186 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.175 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.063 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_xyhbond_nbd_other 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing