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APE1 Y269A phosphorothioate substrate complex with abasic DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 27% PEG 3350, 100 mM Bis Tris Propane (pH 6.5), 200 mM Sodium Fluoride
Crystal Properties Matthews coefficient Solvent content 2.96 58.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.659 α = 90 b = 148.315 β = 90 c = 153.235 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2019-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.77 48.29 100 0.261 7.4 6.8 27446 56.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.77 2.92 100 2.67 0.395 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5DFF 2.77 48.29 1.33 27026 1267 98.68 0.224 0.2214 0.2228 0.2741 0.2747 53.9
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 28.8591 f_angle_d 1.4316 f_chiral_restr 0.0891 f_bond_d 0.0175 f_plane_restr 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4380 Nucleic Acid Atoms 1691 Solvent Atoms 39 Heterogen Atoms
Software Software Software Name Purpose Coot model building PHENIX refinement Blu-Ice data collection XDS data scaling PHENIX phasing XDS data reduction