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ATAD2 in complex with PepLite-Glu
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 = 79.288 α = 90 b = 79.288 β = 90 c = 138.015 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 1.43 61.48 99.5 0.086 0.091 0.027 0.999 17.3 19.5 47816
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 1.43 1.45 2.943 3.252 1.353 0.195 10.3
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 1.43 61.48 47744 2335 99.34 0.196 0.1951 0.1952 0.2135 0.2135 34.361
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] 0.162 0.081 0.162 -0.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.342 r_dihedral_angle_3_deg 15.232 r_dihedral_angle_4_deg 14.137 r_lrange_it 12.973 r_scangle_it 9.067 r_scbond_it 6.192 r_dihedral_angle_1_deg 4.547 r_mcangle_it 4.385 r_mcbond_it 3.024 r_angle_refined_deg 2.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.342 r_dihedral_angle_3_deg 15.232 r_dihedral_angle_4_deg 14.137 r_lrange_it 12.973 r_scangle_it 9.067 r_scbond_it 6.192 r_dihedral_angle_1_deg 4.547 r_mcangle_it 4.385 r_mcbond_it 3.024 r_angle_refined_deg 2.633 r_symmetry_nbd_refined 0.639 r_symmetry_xyhbond_nbd_refined 0.498 r_nbtor_refined 0.321 r_xyhbond_nbd_refined 0.319 r_nbd_refined 0.233 r_chiral_restr 0.151 r_bond_refined_d 0.019 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling xia2 data reduction PHASER phasing