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Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli in complex with AP-site containing DNA substrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K3W
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 3.58 61.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.184 α = 90 b = 76.184 β = 90 c = 164.54 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 ADSC QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.100 NSLS X26C
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 1.4 30 0.064 11.6 7 91763
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 69.8 0.375
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-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION throughout THROUGHOUT 1k3w 1.4 30 91763 91763 4863 95.8 0.16 0.1563 0.2043 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 15 2961.85
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.084 s_non_zero_chiral_vol 0.076 s_zero_chiral_vol 0.06 s_similar_adp_cmpnt 0.06 s_angle_d 0.034 s_from_restr_planes 0.0248 s_anti_bump_dis_restr 0.021 s_bond_d 0.014 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2032 Nucleic Acid Atoms 483 Solvent Atoms 412 Heterogen Atoms 32
Software Software Software Name Purpose SHELX model building SHELXL-97 refinement ADSC data collection DENZO data reduction SCALEPACK data scaling SHELX phasing