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ATAD2 in complex with PepLite-Gly
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 4.1 69.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.772 α = 90 b = 79.772 β = 90 c = 137.872 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 0.9116 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 1.9 48.8 100 0.259 0.266 0.058 0.999 14.3 38.9 21195
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 1.9 1.94 5.046 5.174 1.142 0.726 38.5
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 1.9 48.8 21134 1026 99.986 0.191 0.1891 0.1888 0.2213 0.2211 36.854
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] -0.24 -0.12 -0.24 0.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.575 r_dihedral_angle_4_deg 18.211 r_dihedral_angle_3_deg 15.872 r_lrange_it 9.848 r_scangle_it 7.397 r_scbond_it 5.634 r_dihedral_angle_1_deg 5.18 r_mcangle_it 4.207 r_mcbond_it 3.188 r_angle_refined_deg 1.867
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.575 r_dihedral_angle_4_deg 18.211 r_dihedral_angle_3_deg 15.872 r_lrange_it 9.848 r_scangle_it 7.397 r_scbond_it 5.634 r_dihedral_angle_1_deg 5.18 r_mcangle_it 4.207 r_mcbond_it 3.188 r_angle_refined_deg 1.867 r_symmetry_nbd_refined 0.409 r_nbtor_refined 0.315 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.192 r_chiral_restr 0.119 r_bond_refined_d 0.013 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing