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ATAD2 in complex with FragLite7
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 = 79.599 α = 90 b = 79.599 β = 90 c = 137.348 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 2019-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.979 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 1.49 68.93 100 0.068 0.072 0.022 1 19 18.8 42789
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 1.49 1.52 2.505 2.815 1.247 0.546 8.4
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 1.49 68.93 42712 2188 99.932 0.207 0.2046 0.2046 0.2424 0.2425 34.025
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] -0.685 -0.342 -0.685 2.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.983 r_lrange_it 16.628 r_lrange_other 16.622 r_dihedral_angle_3_deg 13.259 r_dihedral_angle_4_deg 12.019 r_scangle_other 11.265 r_scangle_it 11.235 r_scbond_other 7.944 r_scbond_it 7.926 r_dihedral_angle_1_deg 4.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.983 r_lrange_it 16.628 r_lrange_other 16.622 r_dihedral_angle_3_deg 13.259 r_dihedral_angle_4_deg 12.019 r_scangle_other 11.265 r_scangle_it 11.235 r_scbond_other 7.944 r_scbond_it 7.926 r_dihedral_angle_1_deg 4.796 r_mcangle_other 3.982 r_mcangle_it 3.979 r_mcbond_it 2.899 r_mcbond_other 2.894 r_angle_refined_deg 1.941 r_angle_other_deg 1.51 r_symmetry_nbd_refined 0.34 r_nbd_other 0.283 r_symmetry_xyhbond_nbd_refined 0.265 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.178 r_xyhbond_nbd_other 0.104 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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 161 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction xia2 data scaling PHASER phasing