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Structure of a mutant of the large fragment of DNA polymerase I from Thermus aquaticus in complex with a blunt-ended DNA and ddATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LWM PDB entry 3LWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 0.05M sodium cacodylate, 0.2M KCl, 0.1M Mg(OAc)2, 20% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.525 α = 90 b = 113.525 β = 90 c = 91.238 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 PIXEL PSI PILATUS 6M Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator 2009-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 1.8 50 99.7 0.072 16.88 9.96 63101 -3 42.02
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 1.8 1.91 98.5 0.767 2.63 10.08
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 MOLECULAR REPLACEMENT PDB entry 3LWM 1.8 48.2 2.05 63101 63101 3133 100 0.166 0.164 0.1629 0.194 0.1923
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] 4.6916 4.6916 -0.4333
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.399 f_angle_d 1.088 f_chiral_restr 0.062 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4280 Nucleic Acid Atoms 485 Solvent Atoms 548 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX model building PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing