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PanDDA analysis group deposition -- Crystal Structure of ATAD2 in complex with RZ201
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 4.08 69.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.97 α = 90 b = 79.97 β = 90 c = 137.25 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 2016-04-26 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 1.83 69.26 100 0.195 0.201 0.046 0.999 14.5 18.8 23669
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 1.83 1.88 100 2.404 2.467 0.548 0.494 20.1 1694
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 1.83 69.26 22440 1170 99.97 0.2193 0.217 0.2844 0.2637 0.3065 RANDOM 32.487
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] 0.09 0.04 0.09 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.935 r_dihedral_angle_3_deg 16.193 r_dihedral_angle_4_deg 14.491 r_dihedral_angle_1_deg 4.918 r_mcangle_it 3.35 r_mcbond_other 1.631 r_angle_refined_deg 1.455 r_mcbond_it 1.455 r_angle_other_deg 1.285 r_chiral_restr 0.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.935 r_dihedral_angle_3_deg 16.193 r_dihedral_angle_4_deg 14.491 r_dihedral_angle_1_deg 4.918 r_mcangle_it 3.35 r_mcbond_other 1.631 r_angle_refined_deg 1.455 r_mcbond_it 1.455 r_angle_other_deg 1.285 r_chiral_restr 0.386 r_bond_refined_d 0.024 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing