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APE1 exonuclease product complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DFF PDB entry 5DFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 7% PEG20000, 100 mM sodium citrate, 15% glycerol, 5 mM calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.6 52.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.869 α = 90 b = 63.528 β = 109.43 c = 90.548 γ = 90
Symmetry Space Group P 1 21 1
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 200K 2016-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.3 25 99.4 0.11 0.124 0.057 11 4.2 58422 43.26
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 2.3 2.34 99.4 0.746 0.939 0.562 0.757 2.5
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 PDB entry 5DFF 2.3 24.521 1.33 58422 3443 86.88 0.2161 0.2127 0.2152 0.27 0.2726 47.8056
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 19.78 f_angle_d 1.161 f_chiral_restr 0.056 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4345 Nucleic Acid Atoms 835 Solvent Atoms 167 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing