☰ Navigation Tabs
ATAD2 in complex with PepLite-Val
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 = 79.158 α = 90 b = 79.158 β = 90 c = 138.043 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 61.4 98.4 0.047 0.049 0.015 0.998 27.9 18.2 56991
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 1.734 2.049 1.068 0.375 6
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 48.686 56917 2822 98.141 0.209 0.2078 0.2079 0.227 0.2266 30.216
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] 0.129 0.065 0.129 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.7 r_dihedral_angle_4_deg 15.868 r_dihedral_angle_3_deg 13.546 r_lrange_it 9.529 r_scangle_it 7.993 r_scbond_it 5.727 r_dihedral_angle_1_deg 4.606 r_mcangle_it 3.622 r_angle_refined_deg 2.601 r_mcbond_it 2.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.7 r_dihedral_angle_4_deg 15.868 r_dihedral_angle_3_deg 13.546 r_lrange_it 9.529 r_scangle_it 7.993 r_scbond_it 5.727 r_dihedral_angle_1_deg 4.606 r_mcangle_it 3.622 r_angle_refined_deg 2.601 r_mcbond_it 2.447 r_symmetry_xyhbond_nbd_refined 0.393 r_nbtor_refined 0.325 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.217 r_symmetry_nbd_refined 0.198 r_chiral_restr 0.129 r_bond_refined_d 0.023 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing