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ATAD2 in complex with PepLite-Arg
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 = 79.37 α = 90 b = 79.37 β = 90 c = 137.288 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 2019-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91162 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 48.57 100 0.115 0.118 0.025 1 19 39.6 41696
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 9.075 9.295 2.005 0.458 40.2
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 1.5 48.57 41617 2028 99.957 0.206 0.2039 0.2362 0.224 35.981
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] -0.291 -0.146 -0.291 0.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.186 r_dihedral_angle_4_deg 18.072 r_dihedral_angle_3_deg 15.452 r_lrange_it 12.222 r_scangle_it 8.953 r_scbond_it 6.569 r_dihedral_angle_1_deg 4.738 r_mcangle_it 4.286 r_mcbond_it 3.069 r_angle_refined_deg 2.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.186 r_dihedral_angle_4_deg 18.072 r_dihedral_angle_3_deg 15.452 r_lrange_it 12.222 r_scangle_it 8.953 r_scbond_it 6.569 r_dihedral_angle_1_deg 4.738 r_mcangle_it 4.286 r_mcbond_it 3.069 r_angle_refined_deg 2.131 r_symmetry_nbd_refined 0.424 r_nbtor_refined 0.32 r_symmetry_xyhbond_nbd_refined 0.3 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.213 r_chiral_restr 0.138 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing