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ATAD2 in complex with FragLite6
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 = 79.777 α = 90 b = 79.777 β = 90 c = 135.692 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 0.976 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 69.09 100 0.136 0.143 0.044 0.999 10 19 41617
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 36.608 17.109 0.373 9
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 1.5 61.644 41542 2074 99.933 0.241 0.2392 0.2415 0.2725 0.2667 41.941
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] -1.488 -0.744 -1.488 4.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.013 r_lrange_it 25.33 r_lrange_other 25.321 r_dihedral_angle_3_deg 14.19 r_dihedral_angle_4_deg 13.158 r_scangle_other 8.105 r_scangle_it 8.098 r_mcangle_other 5.55 r_mcangle_it 5.547 r_dihedral_angle_1_deg 5.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.013 r_lrange_it 25.33 r_lrange_other 25.321 r_dihedral_angle_3_deg 14.19 r_dihedral_angle_4_deg 13.158 r_scangle_other 8.105 r_scangle_it 8.098 r_mcangle_other 5.55 r_mcangle_it 5.547 r_dihedral_angle_1_deg 5.44 r_scbond_it 5.279 r_scbond_other 5.272 r_mcbond_it 4.018 r_mcbond_other 4.007 r_angle_refined_deg 1.686 r_angle_other_deg 1.387 r_symmetry_nbd_refined 0.878 r_nbd_other 0.45 r_symmetry_xyhbond_nbd_refined 0.273 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.173 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.031 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction xia2 data scaling PHASER phasing