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ATAD2 in complex with Acetyl-Lys
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 4.02 69.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.029 α = 90 b = 79.029 β = 90 c = 137.875 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 2019-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91162 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 1.76 48.57 100 0.15 0.153 0.033 1 19.6 39.2 26026
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 1.76 1.79 10.637 2.295 0.327 40.4
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 1.76 48.57 25962 1345 99.958 0.206 0.2047 0.2047 0.2271 0.2268 42.31
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] -0.419 -0.209 -0.419 1.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.459 r_dihedral_angle_4_deg 16.635 r_dihedral_angle_3_deg 15.665 r_lrange_it 11.515 r_scangle_it 9.461 r_scbond_it 6.64 r_dihedral_angle_1_deg 5.51 r_mcangle_it 5.477 r_mcbond_it 4.142 r_angle_refined_deg 2.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.459 r_dihedral_angle_4_deg 16.635 r_dihedral_angle_3_deg 15.665 r_lrange_it 11.515 r_scangle_it 9.461 r_scbond_it 6.64 r_dihedral_angle_1_deg 5.51 r_mcangle_it 5.477 r_mcbond_it 4.142 r_angle_refined_deg 2.046 r_symmetry_xyhbond_nbd_refined 0.475 r_nbtor_refined 0.322 r_nbd_refined 0.228 r_xyhbond_nbd_refined 0.194 r_symmetry_nbd_refined 0.16 r_chiral_restr 0.135 r_bond_refined_d 0.013 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing