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Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and dCTP-dA Mismatch (tautomer) in Closed Conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HVI PDB entry 2HVI with insertion site base pair, metal ions, waters, and protein residues 680-717 deleted
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 290 Ammonium Sulfate, MPD, MgSO4, MnSO4, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.59 52.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.91 α = 90 b = 108.96 β = 90 c = 150.13 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 225 mm CCD 2010-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM
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 1.73 100 98.3 0.058 17.99 5.8 160634 157944 -3
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 1.73 1.83 99.6 0.583 2.6
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 FOURIER SYNTHESIS PDB entry 2HVI with insertion site base pair, metal ions, waters, and protein residues 680-717 deleted 1.73 34.242 2.35 160634 149632 6687 93.17 0.1965 0.1952 0.1957 0.2236 0.2246 Inherited free reflections from 2HVI plus randomly generated reflections beyond 1.98 resolution
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] 0.4566 0.5793 -1.0359
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.108 f_angle_d 1.193 f_chiral_restr 0.068 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9119 Nucleic Acid Atoms 848 Solvent Atoms 1368 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling