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Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The WT enzyme at 2.8 resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K3X The NEI protein from PDB 1K3X.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 0.16M calcium acetate, 0.08M sodium cacodylate pH 6.5, 14.4% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 3.27 62.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.721 α = 90 b = 79.578 β = 90 c = 169.653 γ = 90
Symmetry Space Group I 2 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 BRANDEIS - B4 2001-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.041 NSLS X25
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 2.6 30 85.2 0.098 2.5 10629 10629 32.2
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 2.6 2.64 88.8 0.518 548
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT The NEI protein from PDB 1K3X. 2.8 29.02 8158 8158 844 81.7 0.216 0.299 RANDOM 54.6
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 c_dihedral_angle_d 23.9 c_scangle_it 10.77 c_mcangle_it 9.94 c_scbond_it 7.27 c_mcbond_it 6.17 c_angle_deg 1.3 c_improper_angle_d 0.76 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2026 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing