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Structure of the large fragment of thermus aquaticus DNA polymerase I in complex with a blunt-ended DNA and ddATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KTQ PDB ENTRY 3KTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 0.05M TRIS HCl, pH 8, 0.2M ammonium chloride, 0.01M calcium chloride and 35% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.592 α = 90 b = 109.592 β = 90 c = 91.037 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 vertically collimating mirror (M1, focus at infinity), followed by a Bartels Monochromator with dual channel cut crystals 2009-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
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 2.186 50 98.9 0.105 18.96 10.61 32557 -3 42.37
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 2.2 2.33 93.4 0.864 2.53 8.08 4863
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3KTQ 2.186 47.455 -3 32553 32553 1639 98.46 0.1857 0.1857 0.1834 0.1807 0.2284 0.2253 RANDOM 52.4
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] 2.176 2.176 -4.352
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.148 f_angle_d 0.851 f_chiral_restr 0.053 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4276 Nucleic Acid Atoms 485 Solvent Atoms 154 Heterogen Atoms 80
Software Software Software Name Purpose PHENIX model building PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing