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ATAD2 in complex with FragLite31
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 Properties Matthews coefficient Solvent content 4.04 69.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.257 α = 90 b = 79.257 β = 90 c = 137.706 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 2019-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.898 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 2.52 68.85 100 0.7 0.717 0.156 0.959 10.7 37.8 9241
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.62 11.298 2.444 0.463 38.8
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 2.52 68.733 9196 434 100 0.205 0.2031 0.2042 0.2399 0.2419 62.564
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] -1.145 -0.572 -1.145 3.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.769 r_dihedral_angle_3_deg 16.57 r_dihedral_angle_4_deg 14.339 r_lrange_it 13.918 r_scangle_it 11.061 r_scbond_it 8.08 r_mcangle_it 7.216 r_dihedral_angle_1_deg 5.454 r_mcbond_it 5.048 r_angle_refined_deg 1.677
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.769 r_dihedral_angle_3_deg 16.57 r_dihedral_angle_4_deg 14.339 r_lrange_it 13.918 r_scangle_it 11.061 r_scbond_it 8.08 r_mcangle_it 7.216 r_dihedral_angle_1_deg 5.454 r_mcbond_it 5.048 r_angle_refined_deg 1.677 r_nbtor_refined 0.329 r_nbd_refined 0.251 r_xyhbond_nbd_refined 0.243 r_symmetry_nbd_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.147 r_chiral_restr 0.12 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction xia2 data scaling PHASER phasing