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Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with aminopentinyl-7-deaza-2-dATP
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 mMTris pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.22 44.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.609 α = 90 b = 108.609 β = 90 c = 90.516 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 CCD MARMOSAIC 225 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.23000 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 2 47.03 99.9 14.43 42038 -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 2 2.12 99.4 1.78 6661
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 2 47.029 1.26 80633 4047 99.9 0.1966 0.1946 0.1906 0.2339 0.2278 random 35.99
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] 8.0089 8.0089 -6.5238
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.532 f_angle_d 0.993 f_chiral_restr 0.05 f_bond_d 0.014 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4282 Nucleic Acid Atoms 568 Solvent Atoms 203 Heterogen Atoms 69
Software Software Software Name Purpose PHENIX model building PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing