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ATAD2 in complex with PepLite-Asp
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, SITTING DROP 6.5 293 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.145 α = 90 b = 79.145 β = 90 c = 137.536 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 1.34 68.54 99.3 0.047 0.05 0.015 1 24.9 17.3 57366
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 1.34 1.36 1.564 1.898 1.053 0.296 5.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3DAI 1.34 68.54 57288 2981 99.195 0.211 0.2099 0.2099 0.2269 0.2269 31.198
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] 0.159 0.08 0.159 -0.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.089 r_dihedral_angle_3_deg 14.49 r_dihedral_angle_4_deg 14.009 r_lrange_it 11.934 r_scangle_it 8.137 r_scbond_it 5.628 r_dihedral_angle_1_deg 4.367 r_mcangle_it 3.711 r_mcbond_it 2.529 r_angle_refined_deg 2.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.089 r_dihedral_angle_3_deg 14.49 r_dihedral_angle_4_deg 14.009 r_lrange_it 11.934 r_scangle_it 8.137 r_scbond_it 5.628 r_dihedral_angle_1_deg 4.367 r_mcangle_it 3.711 r_mcbond_it 2.529 r_angle_refined_deg 2.264 r_nbtor_refined 0.322 r_symmetry_xyhbond_nbd_refined 0.29 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.217 r_symmetry_nbd_refined 0.19 r_chiral_restr 0.127 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 180 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing