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Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EA0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 1.8M ammonium sulfate, 0.1M sodium acetate pH 4.6-5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.09 60.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.556 α = 90 b = 73.556 β = 90 c = 170.113 γ = 90
Symmetry Space Group P 43 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 CCD MAR CCD 165 mm 2001-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B 1.102 APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 40 98.9 0.099 7.4 13 39078 39078 29.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 96 0.491
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2EA0 1.85 20.41 36395 1831 89.4 0.24 0.24 0.267 RANDOM 40.9
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] 2.97 2.97 -5.93
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.8 c_scangle_it 2.74 c_mcangle_it 1.98 c_scbond_it 1.86 c_mcbond_it 1.31 c_angle_deg 1.2 c_improper_angle_d 0.91 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2039 Nucleic Acid Atoms 461 Solvent Atoms 243 Heterogen Atoms 36
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing