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ATAD2 in complex with PepLite-Tyr
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 = 79.297 α = 90 b = 79.297 β = 90 c = 138.39 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 1.47 61.52 99.4 0.088 0.093 0.027 0.999 16.8 20.5 44189
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 1.47 1.5 4.861 5.255 1.903 0.254 13.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DAI 1.47 61.52 44128 2213 99.273 0.202 0.201 0.2176 0.2324 35.912
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] 0.124 0.062 0.124 -0.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.851 r_dihedral_angle_4_deg 15.078 r_dihedral_angle_3_deg 14.654 r_lrange_it 11.23 r_scangle_it 8.455 r_scbond_it 5.982 r_dihedral_angle_1_deg 4.427 r_mcangle_it 4.201 r_mcbond_it 2.904 r_angle_refined_deg 2.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.851 r_dihedral_angle_4_deg 15.078 r_dihedral_angle_3_deg 14.654 r_lrange_it 11.23 r_scangle_it 8.455 r_scbond_it 5.982 r_dihedral_angle_1_deg 4.427 r_mcangle_it 4.201 r_mcbond_it 2.904 r_angle_refined_deg 2.393 r_symmetry_nbd_refined 0.474 r_symmetry_xyhbond_nbd_refined 0.436 r_nbtor_refined 0.32 r_xyhbond_nbd_refined 0.247 r_nbd_refined 0.226 r_chiral_restr 0.139 r_bond_refined_d 0.025 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing