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ATAD2 in complex with FragLite3
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 293 0.1M HEPES pH 7.0, 2.4 AmSO4, ATAD2~5 mg mL-1.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.205 α = 90 b = 79.205 β = 90 c = 137.91 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 0.97959 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 1.35 68.96 99.7 0.055 0.058 0.017 1 22.9 19.8 56615
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 1.35 1.37 3.9 4.317 1.813 0.204 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 1.35 68.688 56534 2936 99.607 0.212 0.2108 0.2106 0.2306 0.2302 32.546
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] 0.024 0.012 0.024 -0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.235 r_dihedral_angle_4_deg 18.919 r_dihedral_angle_3_deg 17.038 r_lrange_it 11.505 r_scangle_it 8.356 r_scbond_it 5.761 r_dihedral_angle_1_deg 4.558 r_mcangle_it 3.992 r_mcbond_it 2.817 r_angle_refined_deg 2.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.235 r_dihedral_angle_4_deg 18.919 r_dihedral_angle_3_deg 17.038 r_lrange_it 11.505 r_scangle_it 8.356 r_scbond_it 5.761 r_dihedral_angle_1_deg 4.558 r_mcangle_it 3.992 r_mcbond_it 2.817 r_angle_refined_deg 2.247 r_nbtor_refined 0.319 r_symmetry_xyhbond_nbd_refined 0.234 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_refined 0.177 r_chiral_restr 0.137 r_bond_refined_d 0.016 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement Aimless data scaling pointless data scaling DIALS data collection DIMPLE phasing Coot model building DIALS data reduction