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PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with PC581
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DAI 3DAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 1.6M Ammonium Sulfate, 0.1M bis-tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 4.2 70.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.452 α = 90 b = 80.452 β = 90 c = 139.758 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 2016-04-23 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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 1.72 27.95 99.6 0.102 0.105 0.024 0.999 24.9 18.9 28869
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 1.72 1.77 95.1 0.966 0.999 0.248 0.835 15.2 1989
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3DAI 1.72 27.91 27372 1437 99.58 0.1602 0.159 0.1803 0.1836 0.197 RANDOM 23.767
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] 0.19 0.09 0.19 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.609 r_dihedral_angle_4_deg 17.034 r_dihedral_angle_3_deg 14.341 r_dihedral_angle_1_deg 4.482 r_mcangle_it 2.585 r_angle_refined_deg 1.892 r_mcbond_it 1.58 r_mcbond_other 1.576 r_angle_other_deg 1.476 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.609 r_dihedral_angle_4_deg 17.034 r_dihedral_angle_3_deg 14.341 r_dihedral_angle_1_deg 4.482 r_mcangle_it 2.585 r_angle_refined_deg 1.892 r_mcbond_it 1.58 r_mcbond_other 1.576 r_angle_other_deg 1.476 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 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 227 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing