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ATAD2 in complex with FragLite33
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 = 79.331 α = 90 b = 79.331 β = 90 c = 137.081 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 2019-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.915 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 1.48 137.08 100 0.072 0.076 0.023 0.999 16 15.9 43256
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 1.48 1.51 1.824 2.21 1.225 0.437 5.6
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 1.48 61.496 43179 2131 99.921 0.208 0.2067 0.2061 0.2367 0.2372 32.147
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] -0.787 -0.393 -0.787 2.552
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.555 r_dihedral_angle_4_deg 17.006 r_dihedral_angle_3_deg 14.272 r_lrange_it 9.94 r_lrange_other 9.937 r_scangle_other 7.374 r_scangle_it 7.356 r_scbond_it 4.879 r_scbond_other 4.86 r_dihedral_angle_1_deg 4.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.555 r_dihedral_angle_4_deg 17.006 r_dihedral_angle_3_deg 14.272 r_lrange_it 9.94 r_lrange_other 9.937 r_scangle_other 7.374 r_scangle_it 7.356 r_scbond_it 4.879 r_scbond_other 4.86 r_dihedral_angle_1_deg 4.712 r_mcangle_it 3.737 r_mcangle_other 3.735 r_mcbond_other 2.745 r_mcbond_it 2.744 r_angle_refined_deg 1.821 r_angle_other_deg 1.505 r_symmetry_xyhbond_nbd_refined 0.27 r_xyhbond_nbd_refined 0.252 r_nbd_refined 0.23 r_nbd_other 0.212 r_symmetry_nbd_other 0.19 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_other 0.097 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.039 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing