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Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddCTP-dA Mismatch (wobble) in Ajar 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, 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, MES, pH 5.8, vapor diffusion, hanging drop, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.59 52.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.68 α = 90 b = 109.19 β = 90 c = 150.46 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 ADSC QUANTUM 315 2008-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.1158 ALS 12.3.1
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 1.58 100 95.4 0.044 21.94 5.4 210662 200999 -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 1.58 1.68 89.5 0.601 2.4
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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS PDB entry 2HVI with insertion site base pair, metal ions, and protein residues 680-717 deleted 1.582 71.099 2.35 210662 188106 8581 89.64 0.212 0.2107 0.2096 0.2391 0.2376
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] -1.4168 0.8279 0.5889
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.19 f_angle_d 1.169 f_chiral_restr 0.063 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9046 Nucleic Acid Atoms 789 Solvent Atoms 1468 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling