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Crystal structure of the large fragment of DNA polymerase I from Thermus aquaticus in ternary complex with 5-(aminopentinyl)-2-dCTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M8S PDB ENTRY 3M8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 18% PEG 8000, 200mM Mg-Formate, 100 mM Tris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.19 43.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.26 α = 90 b = 108.26 β = 90 c = 90.07 γ = 120
Symmetry Space Group P 31 2 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 CCD MARMOSAIC 225 mm CCD 2011-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99987 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.886 47.15 98.6 12.77 49434 48761 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.94 82 1.83 3643
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION Difference Fourier Techniques THROUGHOUT PDB ENTRY 3M8S 1.886 46.878 2 48759 2442 98.64 0.1875 0.1859 0.1837 0.2162 0.2131 randoom 30.653
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] 9.3973 9.3973 2.3756
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.041 f_angle_d 0.992 f_chiral_restr 0.062 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4260 Nucleic Acid Atoms 570 Solvent Atoms 248 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX model building PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing