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ATAD2 in complex with FragLite23
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 = 79.521 α = 90 b = 79.521 β = 90 c = 137.408 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 1.44 68.87 99.9 0.058 0.06 0.018 1 20.5 19.6 47120
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 1.44 1.47 3.99 4.413 1.868 0.337 10.5
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 (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 1.44 68.87 47049 2316 99.79 0.221 0.22 0.2205 0.2437 0.2445 33.702
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] -0.477 -0.238 -0.477 1.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.904 r_dihedral_angle_3_deg 15.021 r_dihedral_angle_4_deg 12.43 r_lrange_it 9.014 r_lrange_other 8.992 r_scangle_other 7.131 r_scangle_it 7.112 r_scbond_it 4.967 r_scbond_other 4.962 r_dihedral_angle_1_deg 4.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.904 r_dihedral_angle_3_deg 15.021 r_dihedral_angle_4_deg 12.43 r_lrange_it 9.014 r_lrange_other 8.992 r_scangle_other 7.131 r_scangle_it 7.112 r_scbond_it 4.967 r_scbond_other 4.962 r_dihedral_angle_1_deg 4.496 r_mcangle_other 4.078 r_mcangle_it 4.076 r_mcbond_it 2.904 r_mcbond_other 2.899 r_angle_refined_deg 2.121 r_angle_other_deg 1.487 r_xyhbond_nbd_refined 0.235 r_symmetry_xyhbond_nbd_refined 0.233 r_symmetry_xyhbond_nbd_other 0.232 r_nbd_refined 0.231 r_nbd_other 0.197 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.172 r_chiral_restr 0.105 r_xyhbond_nbd_other 0.093 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 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 127 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction xia2 data scaling PHASER phasing