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Crystal structure of a trapped reaction intermediate of the DNA repair enzyme Endonuclease VIII with Brominated-DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K3W pdb entry 1k3w
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 1.8M Ammonium-Sulfate, 0.1M Sodium-citrate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.99 61.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.495 α = 90 b = 76.495 β = 90 c = 164.31 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 BRANDEIS - B4 2001-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.25 40 97.4 0.06 9.7 7.5 131559
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 1.25 1.27 91 0.34 7.5
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 AB INITIO PHASING FREE R pdb entry 1k3w 1.25 10 120771 120771 6452 97.4 0.1491 0.1807 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 8 2941.52
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.104 s_zero_chiral_vol 0.1 s_non_zero_chiral_vol 0.097 s_similar_adp_cmpnt 0.059 s_angle_d 0.04 s_from_restr_planes 0.0271 s_anti_bump_dis_restr 0.027 s_bond_d 0.016 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2023 Nucleic Acid Atoms 401 Solvent Atoms 488 Heterogen Atoms 50
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX model building SHELXL-97 refinement SHELX phasing