☰ Navigation Tabs
ATAD2 in complex with FragLite29
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 3.99 69.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.16 α = 90 b = 79.16 β = 90 c = 136.456 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 2019-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.915 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 1.93 68.55 100 0.142 0.149 0.045 0.999 13 19.7 19756
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 1.93 1.98 2.784 2.945 0.955 0.66 17.6
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 1.93 68.55 19675 1003 99.853 0.2 0.1973 0.2023 0.2453 0.2496 40.093
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] -0.103 -0.051 -0.103 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.976 r_dihedral_angle_4_deg 17.396 r_dihedral_angle_3_deg 15.367 r_lrange_it 11.892 r_lrange_other 11.888 r_scangle_it 8.336 r_scangle_other 8.331 r_scbond_it 5.634 r_scbond_other 5.634 r_mcangle_it 5.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.976 r_dihedral_angle_4_deg 17.396 r_dihedral_angle_3_deg 15.367 r_lrange_it 11.892 r_lrange_other 11.888 r_scangle_it 8.336 r_scangle_other 8.331 r_scbond_it 5.634 r_scbond_other 5.634 r_mcangle_it 5.252 r_mcangle_other 5.248 r_dihedral_angle_1_deg 5.175 r_mcbond_other 4.039 r_mcbond_it 4.035 r_angle_refined_deg 1.787 r_angle_other_deg 1.429 r_symmetry_nbd_refined 0.398 r_nbd_other 0.232 r_xyhbond_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_refined 0.218 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.175 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction xia2 data scaling PHASER phasing